scholarly journals In-Silico Study of Some Natural Plant Phyto-compounds for the Identification of Novel Potent Cholinesterase Inhibitors Against Alzheimer Disease

2021 ◽  
Author(s):  
Dhiraj Kumar ◽  
Sanjana Bhagat
Keyword(s):  
Binding Affinity ◽  
In Silico ◽  
Docking Study ◽  
Inhibitory Effect ◽  
Ache Inhibitor ◽  
Site Analysis ◽  
Strong Binding ◽  
In Silico Studies ◽  
Potent Inhibitory Effect ◽  
Autodock 4.0

The main aim of this study is to identify inhibitory binding potent of the available commercially alkaloids, against the crystal structure of acetylcholinesterase (AChE) protein by in silico studies. The inhibitory data of the compounds should be compared with the internal ligand as well as standard AChE inhibitor Aricept (which is used for the treatment of all stages of Alzheimer’s disease). AutoDock 4.0 is used for the docking study, conformational orientation site analysis, and, with the help of docking, we have calculated parameters like binding energy and inhibition constant. Docking's study showed that Glabridin, Isorosmanol, Quercetin, Honokiol, Eckol, Sargaquinoic acid, and Ginsedosides revealed strong binding affinity with the enzyme. Moreover, The ADMET profiling and physicochemical properties of the selected compounds are evaluated using the Molinspiration and Data warrior software. By showing a strong binding affinity value, positive bioactivity score, and good pharmacokinetic properties, the top compound was determined. After evaluation with all parameters, the compound Glabridin and Ginsedosides show the most potent inhibitory effect towards the acetylcholinesterase, so this compound could be used as a novel is required to treat Alzheimer's disease.

In-silico study of some natural plant phyto-compounds for the identification of novel potent cholinesterase inhibitors against Alzheimer's Disease

2021 ◽  
Vol 12 (3) ◽  
pp. 243-250
Author(s):  
Dhiraj Kumar ◽  
Sanjana Bhagat
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Binding Affinity ◽  
In Silico ◽  
Docking Study ◽  
Inhibitory Effect ◽  
Ache Inhibitor ◽  
Strong Binding ◽  
In Silico Studies ◽  
Autodock 4.0

The main aim of this study is to identify inhibitory binding potent of the available commercially alkaloids, against the crystal structure of acetylcholinesterase (AChE) protein by in silico studies. The inhibitory data of the compounds should be compared with the internal ligand as well as standard AChE inhibitor Aricept (which is used for the treatment of all stages of Alzheimer’s disease). AutoDock 4.0 is used for the docking study, conformational orientation site analysis, and, with the help of docking, we have calculated parameters like binding energy and inhibition constant. Docking's study showed that Glabridin, Isorosmanol, Quercetin, Honokiol, Eckol, Sargaquinoic acid, and Ginsedosides revealed strong binding affinity with the enzyme. Moreover, The ADMET profiling and physicochemical properties of the selected compounds are evaluated using the Molinspiration and Data warrior software. By showing a strong binding affinity value, positive bioactivity score, and good pharmacokinetic properties, the top compound was determined. After evaluation with all parameters, the compound Glabridin and Ginsedosides show the most potent inhibitory effect towards the acetylcholinesterase, so this compound could be used as a novel is required to treat Alzheimer's disease.

scholarly journals Ethers and esters derived from apocynin avoid the interaction between p47phox and p22phox subunits of NADPH oxidase: evaluation in vitro and in silico

2013 ◽  
Vol 33 (4) ◽  
Author(s):  
Martha Edith Macías-Pérez ◽  
Federico Martínez-Ramos ◽  
Itzia Irene Padilla-Martínez ◽  
José Correa-Basurto ◽  
Lowell Kispert ◽  
...  
Keyword(s):  
Nadph Oxidase ◽  
In Silico ◽  
Transmembrane Protein ◽  
Vascular Diseases ◽  
Docking Study ◽  
Free Radical Scavengers ◽  
Phenyl Ester ◽  
Paramagnetic Resonance ◽  
In Silico Studies

NOX (NADPH oxidase) plays an important role during several pathologies because it produces the superoxide anion (O2•−), which reacts with NO (nitric oxide), diminishing its vasodilator effect. Although different isoforms of NOX are expressed in ECs (endothelial cells) of blood vessels, the NOX2 isoform has been considered the principal therapeutic target for vascular diseases because it can be up-regulated by inhibiting the interaction between its p47phox (cytosolic protein) and p22phox (transmembrane protein) subunits. In this research, two ethers, 4-(4-acetyl-2-methoxy-phenoxy)-acetic acid (1) and 4-(4-acetyl-2-methoxy-phenoxy)-butyric acid (2) and two esters, pentanedioic acid mono-(4-acetyl-2-methoxy-phenyl) ester (3) and heptanedioic acid mono-(4-acetyl-2-methoxy-phenyl) ester (4), which are apocynin derivatives were designed, synthesized and evaluated as NOX inhibitors by quantifying O2•− production using EPR (electron paramagnetic resonance) measurements. In addition, the antioxidant activity of apocynin and its derivatives were determined. A docking study was used to identify the interactions between the NOX2′s p47phox subunit and apocynin or its derivatives. The results showed that all of the compounds exhibit inhibitory activity on NOX, being 4 the best derivative. However, neither apocynin nor its derivatives were free radical scavengers. On the other hand, the in silico studies demonstrated that the apocynin and its derivatives were recognized by the polybasic SH3A and SH3B domains, which are regions of p47phox that interact with p22phox. Therefore this experimental and theoretical study suggests that compound 4 could prevent the formation of the complex between p47phox and p22phox without needing to be activated by MPO (myeloperoxidase), this being an advantage over apocynin.

scholarly journals Marine derivatives prevent w MUS81 in silico studies

2021 ◽  
Vol 8 (9) ◽  
pp. 210974
Author(s):  
Son Tung Ngo ◽  
Khanh B. Vu ◽  
Minh Quan Pham ◽  
Nguyen Minh Tam ◽  
Phuong-Thao Tran
Keyword(s):  
Binding Affinity ◽  
Binding Free Energy ◽  
Dominant Factor ◽  
Cancer Drug ◽  
Perturbation Approach ◽  
Strong Binding ◽  
In Silico Studies ◽  
Marine Compounds ◽  
Aspergiolide A ◽  
Dynamics Simulations

The winged-helix domain of the methyl methanesulfonate and ultraviolet-sensitive 81 ( w MUS81) is a potential cancer drug target. In this context, marine fungi compounds were indicated to be able to prevent w MUS81 structure via atomistic simulations. Eight compounds such as D197 ( Tryptoquivaline U ), D220 ( Epiremisporine B ), D67 ( Aspergiolide A ), D153 ( Preussomerin G ), D547 ( 12,13-dihydroxyfumitremorgin C ), D152 ( Preussomerin K ), D20 ( Marinopyrrole B ) and D559 ( Fumuquinazoline K ) were indicated that they are able to prevent the conformation of w MUS81 via forming a strong binding affinity to the enzyme via perturbation approach. The electrostatic interaction is the dominant factor in the binding process of ligands to w MUS81. The residues Trp55, Arg59, Leu62, His63 and Arg69 were found to frequently form non-bonded contacts and hydrogen bonds to inhibitors. Moreover, the influence of the ligand D197 , which formed the lowest binding free energy to w MUS81, on the structural change of enzyme was investigated using replica exchange molecular dynamics simulations. The obtained results indicated that D197 , which forms a strong binding affinity, can modify the structure of w MUS81. Overall, the marine compounds probably inhibit w MUS81 due to forming a strong binding affinity to the enzyme as well as altering the enzymic conformation.

scholarly journals Chrysophanol, Physcion, Hesperidin and Curcumin Modulate the Gene Expression of Pro-Inflammatory Mediators Induced by LPS in HepG2: In Silico and Molecular Studies

Antioxidants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 371 ◽  
Author(s):  
Selim ◽  
Elgazar ◽  
Abdel-Hamid ◽  
El-Magd ◽  
Yasri ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatocellular Carcinoma ◽  
Traditional Medicine ◽  
In Silico ◽  
Docking Study ◽  
Mitogen Activated Protein Kinase ◽  
Dependent Manner ◽  
Molecular Docking Study ◽  
Necrosis Factor Alpha ◽  
In Silico Studies

Hepatitis is an inflammatory condition that can develop hepatocellular carcinoma. Traditional medicine has always been the pillar of medical practice. However, it became less compatible with the current understanding of the diseases and the possible treatment. Therefore, in silico tools could be utilized for building the bridge between the legacy of the past and the current medical approaches allowing access to new therapeutic discoveries. In this work, a Chinese traditional medicine database was screened using structure-based virtual screening to identify molecules that could inhibit p38 alpha mitogen-activated protein kinase (MAPK). Out of the identified compounds, four selected compounds: chrysophanol, physcion, curcumin and hesperidin were isolated from their respective sources and their structures were confirmed by spectroscopic methods. These compounds decreased the gene expression of tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6) and interleukin-1beta (IL-1β) in lipopolysaccharide (LPS) induced inflammation in a hepatocellular carcinoma cell line (HepG2) in a dose-dependent manner. The molecular docking study revealed the specificity of these compounds towards p38 MAPK rather than other MAPKs. In conclusion, the molecular and in silico studies suggest that the isolated compounds could be a potential treatment for hepatitis by resolving inflammation controlled by MAPKs, thus limiting the development of further complications and lower side effects.

In silico Molecular Docking Study to Search New SGLT2 Inhibitor based on Dioxabicyclo[3.2.1] Octane Scaffold

2020 ◽  
Vol 16 (2) ◽  
pp. 145-154 ◽  
Author(s):  
Shubham Kumar ◽  
Gopal L. Khatik ◽  
Amit Mittal
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
In Silico ◽  
Promising Result ◽  
Sglt2 Inhibitor ◽  
Docking Study ◽  
Sglt2 Inhibitors ◽  
Molecular Structures ◽  
Molecular Docking Study ◽  
Us Fda

Background: Diabetes is a leading cause of high mortality rate in the world. Recently, SGLT2 inhibitors showed the promising result to treat diabetes and therefore several molecules are approved by the US FDA. Objective: SGLT2 inhibitors were designed based on dioxabicyclo[3.2.1] octane with the aim to search new lead molecule. Methods: The molecular structures were drawn in ChemBiodraw ultra and molecular docking study was performed by AutoDock Vina 1.5.6 software. The LogP and toxicity were predicted online using AlogP and Lazar in-silico respectively. Results: Among all the designed molecules, SK306 showed the maximum binding affinity against the 3dh4 SGLT2 protein of Vibrio parahaemolyticus. LogP values were also calculated in order to determine the lipophilic property of the best binding molecules which show LogP 2.82-3.79 in the range for good absorption and elimination, also predicted to be non-toxic. Conclusion: SGLT2 inhibitors were designed based on the dioxabicyclo [3.2.1] octane resulting in a new lead molecule with high binding affinity; also these molecules were predicted to be noncarcinogenic with low LogP.

The Inhibitory Effect of Three Essential Oils on Candida rugosa Lipase: In Vitro and In Silico Studies

2020 ◽  
Vol 10 (3) ◽  
pp. 208-215 ◽  
Author(s):  
Talia Serseg ◽  
Khedidja Benarous ◽  
Mohamed Yousfi
Keyword(s):  
Molecular Docking ◽  
Essential Oils ◽  
In Silico ◽  
Candida Rugosa ◽  
Inhibitory Effect ◽  
Mentha Piperita ◽  
Inhibition Mechanism ◽  
Syzygium Aromaticum ◽  
In Silico Studies

Background: Essential oils have been used for centuries. EOs are gaining increasing interest because of their acceptance by consumers and their safe status. For the first time, the effect of essential oils on the inhibition of lipases has been investigated in this work. Objective: We aimed in this study to investigate in vitro the inhibitory effects of the three essential oils of most used spices: Peppermint (Mentha piperita L.), cinnamon (Cinnamomum zeylanicum L.) and Cloves (Syzygium aromaticum L. Merr. et Perry) against Candida rugose lipase. In silico studies using molecular docking have been achieved to study the inhibition mechanism of major compounds of EO: menthol, carvacrol, eugenol and cinnamylaldehyde toward CRL. Methods: The inhibitory effect of three essential oils were determined by candida rugosa enzyme and pNP-L as substrate using spectrophotometry. Autodock vina was used for molecular docking with 50 runs. Results: We have found that these essential oils have a strong inhibitory effect with IC50 values 1.09, 1.78 and 1.13 mg/ml compared with Orlistat 0.06 mg/ml. The results show competitive inhibition for the three major compounds Menthol, Carvacrol and Eugenol with uncompetitive inhibition for Cinnamaldehyde. Different repetition ratios of hydrogen bonds and hydrophobic interactions were observed. The saved interactions were with His449, Ser209, Gly123, Gly124 and Phe344 for all molecules. Conclusion: These observations support using and considering essential oils and their major compounds as good sources for design new drugs to treat candidiasis and other diseases related to Lipases.

scholarly journals Molecular Docking Studies of a Cyclic Octapeptide-Cyclosaplin from Sandalwood

2019 ◽  
Author(s):  
Abheepsa Mishra ◽  
Satyahari Dey
Keyword(s):  
Molecular Docking ◽  
Protein Kinase ◽  
Protein Kinases ◽  
Binding Affinity ◽  
In Silico ◽  
Docking Studies ◽  
Screening Methods ◽  
Large Set ◽  
Strong Binding ◽  
Related Proteins

Natural products from plants such as, chemopreventive agents attract huge attention because of their low toxicity and high specificity. The rational drug design in combination with structure based modeling and rapid screening methods offer significant potential for identifying and developing lead anticancer molecules. Thus, the molecular docking method plays an important role in screening a large set of molecules based on their free binding energies and proposes structural hypotheses of how the molecules can inhibit the target. Several peptide based therapeutics have been developed to combat several health disorders including cancers, metabolic disorders, heart-related, and infectious diseases. Despite the discovery of hundreds of such therapeutic peptides however, only few peptide-based drugs have made it to the market. Moreover, until date the activities of cyclic peptides towards molecular targets such as protein kinases, proteases, and apoptosis related proteins have never been explored. In this study we explore the in silico kinase and protease inhibitor potentials of cyclosaplin as well as study the interactions of cyclosaplin with other cancer-related proteins. Previously, the structure of cyclosaplin was elucidated by molecular modeling associated with dynamics that was used in the current study. Docking studies showed strong affinity of cyclosaplin towards cancer-related proteins. The binding affinity closer to 10 indicated efficient binding. Cyclosaplin showed strong binding affinities towards protein kinases such as EGFR, VEGFR2, PKB and p38 indicating its potential role in protein kinase inhibition. Moreover, it displayed strong binding affinity to apoptosis related proteins and revealed the possible role of cyclosaplin in apoptotic cell death. The protein-ligand interactions using LigPlot displayed some similar interactions between cyclosaplin and peptide-based ligands especially in case of protein kinases and a few apoptosis related proteins. Thus, the in silico analyses gave an insight of cyclosaplin as a potential apoptosis inducer and protein kinase inhibitor.

Synthesis, antineoplastic activity and in silico studies of (S)-N-(1-hydroxy-3-methylbutan-2-yl)-3-(p-tolyl)-1,2,4-oxadiazole-5-carboxamide

2021 ◽  
Vol 25 (7) ◽  
pp. 167-176
Author(s):  
Cláudia Laís Araújo Almeida Santos ◽  
Jonh Anderson Macêdo Santos ◽  
Rodrigo Ribeiro Alves Caiana ◽  
Silvia Maria Souza ◽  
Jucleiton José Rufino Freitas ◽  
...  
Keyword(s):  
In Silico ◽  
Low Cost ◽  
Docking Study ◽  
New Drugs ◽  
Molecular Docking Study ◽  
Traditional Medicines ◽  
In Silico Studies ◽  
In Silico Study ◽  
Pharmacokinetic Properties ◽  
Low Toxicity

The development of chemotherapy agents without side effects is a major challenge, since traditional medicines usually have undesirable properties such as high toxicity, resistance and low bioavailability. In this sense, computational methods play a crucial role in the discovery and optimization of new drugs, as they combine speed and efficiency with low cost. The 1,2,4-oxadiazoles are one of the main classes of heterocyclics due to their numerous biological applications. In this work, we report the synthesis, antineoplastic evaluation and in silico study of a new 1,2,4-oxadiazole. The (S)-N-(1-hydroxy-3-methylbutan-2-yl)-3-(p-toluyl)-1,2,4-oxadiazole-5-carboxamide was obtained after two reaction steps in excellent yield. Although it has shown low activity in relation to the MCF-7, HCT116 and HL60 tumor cell lines, the molecular docking study indicates that this compound acts in the colchicine site and can inhibit tubulin polymerization. From the calculation of pharmacokinetic properties by the SwissADME and Osiris Property Explorer programs, it is possible to infer that the compound meets the Lipinski rules presenting good oral bioavailability and low toxicity.

The inhibitory Effects of Some Artificial Food Colorings on α-amylase and α-glucosidase: In Vitro and In Silico Studies

2021 ◽  
Vol 17 ◽  
Author(s):  
Reguia Mahfoudi ◽  
Amar Djeridane ◽  
Djilali Tahri ◽  
Mohamed Yousfi
Keyword(s):  
In Silico ◽  
Hydrophobic Interactions ◽  
Inhibitory Effect ◽  
Docking Studies ◽  
Qsar Study ◽  
Molegro Virtual Docker ◽  
Artificial Food ◽  
In Silico Studies ◽  
Ic50 Values

Background: Inhibition of α-amylase and α-glucosidase is considered as an important therapeutic target to manage type 2 diabetes mellitus (T2DM), reducing postprandial hyperglycemia (PPHG). Objective: The present work explored the antidiabetic activities of five artificial food colorings by α-amylase and α-glucosidase enzyme inhibition in vitro and in Silico. Methods: In this study, inhibition of α-amylase and α-glucosidase were evaluated. Further, the interaction between enzymes (α-amylase and α-glucosidase) and ligands (food colorings) was followed by QSAR and molecular docking studies. Results: The in vitro results obtained show that the blue patent (SIN131) exhibited more potent inhibition with IC50 values of 0.03± 0.01 mM and 0.014±0.001 mM against α-amylase and α-glucosidase inhibition respectively compared to acarbose. The QSAR study found a strong correlation between IC50 values with four molecular descriptors. This linear regression confirms that a strong polarity (Apol) and a low hydrophobia (ALogP) favor the inhibitory effect of these colorings toward both enzymes. Also, a negative role of the number of heavy atoms has been demonstrated in the phenomenon of inhibition of this enzyme. Finally, the descriptor εlumo (electronic affinity) plays a crucial role on the inhibitory power of these dyes toward both enzymes by electron transfer. The virtual screening of the inhibition of α-amylase and α-glucosidase by these colorings, using Molegro Virtual Docker (MVD), allowed us to obtain stable complexes with interaction energies resulting from the place of hydrogen bonds and several hydrophobic interactions. However, the sulfonate groups of these colorings can be the major factors in the inhibition of these enzymes. On the other hand, Rerank Score with the pose are perfectly correlated (R2> 0.76) to the inhibitory activity of these food colorings measured experimentally. Conclusion: The present study suggests that the Blue Patent V (SIN131) effectively act as α-amylase and α-glucosidase inhibitor leading to a reduction in starch hydrolysis and hence eventually to lowered glucose levels.

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