scholarly journals Molecular Interaction Analysis of COX-2 against Curcuminoid and Xanthorizol Ligand as Anti Breast Cancer using Molecular Docking

2017 ◽  
Vol 2 (3) ◽  
pp. 139-149
Author(s):  
Ridho Pratama ◽  
Laksmi Ambarsari ◽  
Tony Ibnu Sumaryada
Keyword(s):  
Breast Cancer ◽  
Amino Acids ◽  
Molecular Docking ◽  
Binding Affinity ◽  
Interaction Analysis ◽  
Competitive Inhibitor ◽  
Common Cancer ◽  
Chemopreventive Effect ◽  
Cox 2 ◽  
Breast Cancer Drugs

Breast cancer is one of the most common cancer in the world that occurs in women. Thedevelopment process of cancer is regulated by a variety of pathways that involve various enzymes. COX-2 is an enzyme involved in the inflammatory process in further stages that will play importantroles in breast cancer cells progression. The uses of natural compound from plants give new hope forbreast cancer treatment with minimal side effects. Temulawak is a potential breast cancer drugs because it contains curcuminoid and xanthorizol. Curcumin and xanthorizol has been reported to have chemopreventive effect on colon cancer development. The drug that has same functions of these compounds needed to be examined with various approaches. One of the approach used in this research is molecular docking. Based on ligand analysis with Lipinski and toxicity test using ADMET, curcuminoid and xanthorizol met criteria as medicinal compounds. Curcumin had the highest binding affinity(?G) with the value -9.3 kcal/mol but still under commercial drug celecoxib binding affinity (?G) = -12,5. There were three hydrogen bonds in amino acid Arg106 and Tyr341 His75 which were amino acids in the active side of COX-2. There were 15 amino acids that have similar ties with commercial drug celecoxib. Based on the binding affinity and binding similiarity, curcuminoid and xanthorizol were predicted as compounds that have potential as competitive inhibitor of COX-2 enzyme.

scholarly journals Molecular Docking and Physicochemical Analysis of the Active Compounds of Soursop (Annona muricata Linn) for an Anti-Breast Cancer Agent

2020 ◽  
Vol 11 (4) ◽  
pp. 11380-11389
Keyword(s):  
Breast Cancer ◽  
Molecular Docking ◽  
Interaction Analysis ◽  
Docking Simulation ◽  
Oral Drug ◽  
Inhibition Mechanism ◽  
Annona Muricata ◽  
Drug Bioavailability ◽  
Cox 2 ◽  
Cancer Agent

Breast cancer cases continue to increase every year. One plant that potentially has the anti-breast-cancer activity is soursop. Some compounds in soursop (Annona muricata Linn) have been reported to inhibit COX-2 enzyme (PDB code: 3LN1) activity. However, each of these test compounds' inhibition potential has not been known really well and still needs to be explored. In this research, the molecular docking simulation and the physicochemical and pharmacochemical descriptor analysis (using SwissADME server) were used to explore the potential of compounds contained in soursop as a COX-2 inhibitor for an anti-breast cancer agent. The results have shown that xylopine can inhibit the COX-2 enzyme activity with a binding energy of -11.9 kcal/mol. Its physicochemical and pharmacochemical descriptors are still within the range of oral drug bioavailability. Molecular interaction analysis has also revealed Val335, Leu338, Ser339, Trp373, Phe504, Val509, Gly512, Ala513, Ser516 amino acids always appear in ligand-COX-2 interaction and predicted to play an important role in the COX-2 inhibition mechanism.

scholarly journals Molecular docking analysis of COX-2 for potential inhibitors

2020 ◽  
Vol 16 (10) ◽  
pp. 753-758
Author(s):  
Jayaraman Selvaraj ◽  
Keyword(s):  
Breast Cancer ◽  
Molecular Docking ◽  
Medicinal Plants ◽  
Cyclooxygenase 2 ◽  
Docking Analysis ◽  
Natural Alkaloid ◽  
Cox 2 ◽  
Potential Inhibitors ◽  
Molecular Docking Analysis

Cyclooxygenase-2 (COX-2) is liked with breast cancer. Therefore, it is of interest to design and develop new yet effective compounds against COX-2 from medicinal plants such as the natural alkaloid compounds. We document the optimal binding features of aristolochicacid with COX-2 protein for further consideration.

scholarly journals Chemical Profiles and Pharmacological Properties with in Silico Studies on Elatostema papillosum Wedd

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 809 ◽  
Author(s):  
Md. Zia Uddin ◽  
Arkajyoti Paul ◽  
Ahmed Rakib ◽  
Saad Ahmed Sami ◽  
Shafi Mahmud ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Serotonin Receptor ◽  
Computational Study ◽  
Biological Activities ◽  
Binding Affinities ◽  
In Silico Studies ◽  
Cox 2 ◽  
Cox 1

The current study attempted, for the first time, to qualitatively and quantitatively determine the phytochemical components of Elatostema papillosum methanol extract and their biological activities. The present study represents an effort to correlate our previously reported biological activities with a computational study, including molecular docking, and ADME/T (absorption, distribution, metabolism, and excretion/toxicity) analyses, to identify the phytochemicals that are potentially responsible for the antioxidant, antidepressant, anxiolytic, analgesic, and anti-inflammatory activities of this plant. In the gas chromatography-mass spectroscopy analysis, a total of 24 compounds were identified, seven of which were documented as being bioactive based on their binding affinities. These seven were subjected to molecular docking studies that were correlated with the pharmacological outcomes. Additionally, the ADME/T properties of these compounds were evaluated to determine their drug-like properties and toxicity levels. The seven selected, isolated compounds displayed favorable binding affinities to potassium channels, human serotonin receptor, cyclooxygenase-1 (COX-1), COX-2, nuclear factor (NF)-κB, and human peroxiredoxin 5 receptor proteins. Phytol acetate, and terpene compounds identified in E. papillosum displayed strong predictive binding affinities towards the human serotonin receptor. Furthermore, 3-trifluoroacetoxypentadecane showed a significant binding affinity for the KcsA potassium channel. Eicosanal showed the highest predicted binding affinity towards the human peroxiredoxin 5 receptor. All of these findings support the observed in vivo antidepressant and anxiolytic effects and the in vitro antioxidant effects observed for this extract. The identified compounds from E. papillosum showed the lowest binding affinities towards COX-1, COX-2, and NF-κB receptors, which indicated the inconsequential impacts of this extract against the activities of these three proteins. Overall, E. papillosum appears to be bioactive and could represent a potential source for the development of alternative medicines; however, further analytical experiments remain necessary.

scholarly journals Hepatoprotective Activity of Pirdot Leaves (Saurauia vulcani Korth) Ethanol Extract in Laboratory Rats (Rattus norvegicus) and Characterization of Bioactive Compounds Using a Molecular Docking Approach

2021 ◽  
Vol 9 (A) ◽  
pp. 1265-1270
Author(s):  
Erlintan Sinaga ◽  
Syafruddin Ilyas ◽  
Salomo Hutahaean ◽  
Panal Sitorus
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Bioactive Compounds ◽  
Ethanol Extract ◽  
Treated Group ◽  
Hepatoprotective Activity ◽  
Tnf Α ◽  
Pomolic Acid ◽  
Docking Approach ◽  
Cox 2

AIM: The hepatoprotective activities of  bioactive compounds Pirdot were investigated in vivo and in silico. METHODS: In this study, the completely randomized design non-factorial was experimentally to assess the value of SGPT and SGOT and twenty four adult male rats were divided into four groups : group G0, control group; group G1, a treated group received 0.1 ml sheep red blood cell; group G2, a treated group received 500 mg ethanol extract Pirdot; group G3, a group treated received 500 mg ethanol extract Pirdot and 0,1 ml sheep red blood cell. On thirty one days of treatment, the blood of all rats group were taken to value SGPT and SGOT using DiaLab kit. Furthermore, the molecular docking study was done to analyse molecular interaction that COX-2 and  TNF-α were the primary target protein of bioactive compounds of Pirdot associated with hepatoprotective activities. In addition, it tends to be the target of non-steroidal anti-inflammatory drugs such as Ibuprofen. RESULTS: The results show SGOT and SGPT value significantly [p<0.05] decreased on Group G2 and G3. Moreover, the bioactive compounds of Pirdot, such as Pomolic acid and Ursolic acid tend to be the potential compound on liver protection. Moreover, Pomolic acid has a good binding affinity -14.6 kcal mol-1 with COX-2 Protein and the binding affinity of cis-3-O-p-hydroxycinnamoyl Ursolic acid was -15.1 kcal mol-1 associated with TNF-α Protein. CONLUSION:  Pirdot Leaves (Saurauia vulcani Korth.)  Ethanol Extract showed Hepatoprotective activity in rats (Rattus norvegicus). Molecular docking approach showed that pomolic acid has a good binding affinity with COX-2 Protein and TNF-α Protein.

scholarly journals In Silico Molecular Docking Studies of Lichen Metabolites against Cyclooxygenase-2 Enzyme

2015 ◽  
Vol 18 (2) ◽  
pp. 90-96 ◽  
Author(s):  
Mohammad Firoz Khan ◽  
Sabreena Aleem Nabila ◽  
Ridwan Bin Rashid ◽  
Mohammad Sharifur Rahman ◽  
Abu Asad Chowdhury ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Usnic Acid ◽  
Cyclooxygenase 2 ◽  
Therapeutic Effects ◽  
Lichen Metabolites ◽  
Cox 2 ◽  
Anti Inflammatory ◽  
Cox 2 Inhibitors

Cyclooxygenase-2 (COX-2) is an inducible enzyme that causes inflammation. COX-2 inhibitors are clinically effective anti-inflammatory agents with less gastrointestinal and renal toxicities. However, they lack anti-thrombotic activity and hence lead to increased incidences of adverse cardiovascular thrombotic events, including myocardial infarction. Therefore, there is still need to develop COX-2 inhibitors with better therapeutic effects and tolerability. The aim of the present study is to explore the anti-inflammatory activity of five lichen metabolites by conducting virtual screenings. In this regard, molecular docking simulations were carried out for the lichen metabolites namely atranorin, diffractic acid, lecanoric acid, salazinic acid and usnic acid with human COX-2 enzyme and the docked results were compared with the standard reference ligands (Celecoxib and Rofecoxib). Among all the docked ligands, the lecanoric acid demonstrated best binding affinity -9.83 kcal/mol followed by atranorin (-8.7 kcal/mol) and diffractic acid (-8.6 kcal/mol) which are comparable to the reference ligands celecoxib (-12.3 kcal/mol) and rofecoxib (-11.2 kcal/mol). The salazinic acid and usnic acid has shown binding affinity of -7.9 kcal/mol and -4.7 kcal/mol, respectively. Moreover, all the ligands except atranorin and diffractic acid satisfied Lipinski’s rule of 5. From the docking results it was revealed that the lichen metabolites might have inhibitory activity against COX-2 enzyme, and are expected to be useful in conducting in vivo anti-inflammatory screenings on animal model which may lead to the development of more effective and potent new chemical entities with anti-inflammatory properties.Bangladesh Pharmaceutical Journal 18(2): 90-96, 2015

scholarly journals Molecular Interaction Analysis of COX-2 Against Aryl Amino Alcohol Derivatives from Isoeugenol as Anti Breast Cancer using Molecular Docking

2021 ◽  
Vol 16 (3) ◽  
pp. 581-587
Author(s):  
Zulfa Zuhrufa ◽  
Tatang Shabur Julianto
Keyword(s):  
Breast Cancer ◽  
Molecular Docking ◽  
Amino Alcohol ◽  
Interaction Analysis ◽  
Data Bank ◽  
Docking Studies ◽  
Hydroxyl Groups ◽  
Cancer Symptoms ◽  
Result Show ◽  
Docking Approach

Breast cancer occurs due to uncontrolled cells proliferation. The Proliferation causes severe inflammatory which can be the initial stages of cancer symptoms. Aryl amino alcohol compounds from isoeugenol derivatives are proposed for the potential drugs of breast cancer. This study was conducted on iso-eugenol derivatives by adding carbonyl groups, hydroxyl groups, halide compounds and amines to determine the effect on anticancer activity through molecular docking studies. The molecular docking approach is carried out to see the interaction of ligands with protein compounds by using the minimized ligand energy bind with protein active site using protein data bank ID 5GMN. The docking result show that IE-Benzanilide-Cl (11) and IE-Benzanilide-OH (10) have the lowest binding energy (−8.3 kcal/mol and −8.6 kcal/mol) compare to another compounds. AdmetSAR computer simulations show that all compounds have very few toxic effects. The use of aryl amino alcohol derivatives (10 and 11) may be suggested as anti-breast cancer drugs. Copyright © 2021 by Authors, Published by BCREC Group. This is an open access article under the CC BY-SA License (https://creativecommons.org/licenses/by-sa/4.0). 

scholarly journals Design of Novel Selective Estrogen Receptor Inhibitors using Molecular Docking and Protein-Ligand Interaction Fingerprint Studies

2021 ◽  
pp. 470-483
Author(s):  
Galla Rajitha ◽  
Murthi Vidya Rani ◽  
Umakanth Naik Vankadoth ◽  
Amineni Umamaheswari
Keyword(s):  
Breast Cancer ◽  
Estrogen Receptor ◽  
Molecular Docking ◽  
Cancer Therapy ◽  
Binding Affinity ◽  
Docking Studies ◽  
Fingerprint Analysis ◽  
Breast Cancer Therapy ◽  
Ligand Interaction ◽  
Human Estrogen Receptor

Aims: The genomic and non-genomic actions of human estrogen receptor α (hERα) play a crucial role in breast epithelial cell proliferation and survival, as well as mammary tumorigenesis. hERα has been proved as a potential target for breast cancer therapy over the last 3 decades. Hence designing novel inhibitors targeting hERα can be a valuable approach in breast cancer therapy. Study Design:  In the present study, the goal is to identify novel hERα inhibitors through molecular docking, AI based virtual screening and interaction fingerprint analysis. Place and Duration of Study: Department of Bioinformatics, Sri Venkateswara Institute of Medical Sciences, Tirupati, Andhra Pradesh, India in between July 2021-sep 2021. Methodology: Molecular docking studies were performed using the human estrogen receptor alpha ligand-binding domain in complex with 4-hydroxytamoxifen (PDB: 3ERT) against existing compounds from literature. The best docked existing compound and co-crystal ligand were subjected to shape screening against 28 million compounds and resulted compounds constituted the hERα inhibitor dataset which was subjected to rigid receptor docking. Further, interaction fingerprint analysis was applied as complimentary method to docking for comparing the similarity of predicted binding poses of proposed leads with that of reference binding pose. Results: Co-crystal ligand (4-OHT) and E99 exhibited better binding affinity among existing ligand set. Rigid receptor docking studies resulted in four lead compounds possessing better docking scores than 4-OHT and E99. Moreover, leads showed favorable absorption, distribution, metabolism, excretion and toxicity properties within the range of 95% FDA approved drugs. Proposed leads showed interactions with binding site residues of hERα similar to that of 4-OHT with better binding affinity. The ability of obtained leads to retrieve actives was validated using receiver operative characteristic (ROC) curve. Conclusion: From above results, it has been observed that the proposed leads have potential to act as novel hERα inhibitors.

scholarly journals Molecular Docking Study of Conformational Polymorph: Building Block of Crystal Chemistry

2013 ◽  
Vol 2013 ◽  
pp. 1-6
Author(s):  
Rashmi Dubey ◽  
Ashish Kumar Tewari ◽  
Ved Prakash Singh ◽  
Praveen Singh ◽  
Jawahar Singh Dangi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Docking ◽  
Binding Affinity ◽  
Crystal Chemistry ◽  
Building Block ◽  
Weak Interactions ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Cox 2

Two conformational polymorphs of novel 2-[2-(3-cyano-4,6-dimethyl-2-oxo-2H-pyridin-1-yl)-ethoxy]-4,6-dimethyl nicotinonitrile have been developed. The crystal structure of both polymorphs (1aand1b) seems to be stabilized by weak interactions. A difference was observed in the packing of both polymorphs. Polymorph1bhas a better binding affinity with the cyclooxygenase (COX-2) receptor than the standard (Nimesulide).

scholarly journals A Molecular Interaction Analysis Reveals the Possible Roles of Graphene Oxide in a Glucose Biosensor

Biosensors ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 18 ◽  
Author(s):  
Tony Sumaryada ◽  
Muhammad Sandy Gunawan ◽  
Salahuddin Perdana ◽  
Sugianto Arjo ◽  
Akhiruddin Maddu
Keyword(s):  
Graphene Oxide ◽  
Molecular Docking ◽  
Binding Affinity ◽  
Active Sites ◽  
Interaction Analysis ◽  
Glucose Sensing ◽  
Glucose Biosensor ◽  
Oxide Surface ◽  
Sensing Mechanism ◽  
Biosensor System

In this paper, we report the molecular docking study of graphene oxide and glucose oxidase (GOx) enzyme for a potential glucose biosensing application. The large surface area and good electrical properties have made graphene oxide as one of the best candidates for an enzyme immobilizer and transducer in the biosensing system. Our molecular docking results revealed that graphene oxide plays a role as a GOx enzyme immobilizer in the glucose biosensor system since it can spontaneously bind with GOx at specific regions separated from the active sites of glucose and not interfering or blocking the glucose sensing by GOx in an enzyme-assisted biosensor system. The strongest binding affinity of GOx-graphene oxide interaction is −11.6 kCal/mol and dominated by hydrophobic interaction. Other modes of interactions with a lower binding affinity have shown the existence of some hydrogen bonds (H-bonds). A possibility of direct sensing (interaction) model of glucose by graphene oxide (non-enzymatic sensing mechanism) was also studied in this paper, and showed a possible direct glucose sensing by graphene oxide through the H-bond interaction, even though with a much lower binding affinity of −4.2 kCal/mol. It was also found that in a direct glucose sensing mechanism, the sensing interaction can take place anywhere on the graphene oxide surface with almost similar binding affinity.

scholarly journals GC–MS Analysis, Molecular Docking and Pharmacokinetic Properties of Phytocompounds from Solanum torvum Unripe Fruits and Its Effect on Breast Cancer Target Protein

2021 ◽  
Author(s):  
R. Saravanan ◽  
K. Raja ◽  
D. Shanthi
Keyword(s):  
Breast Cancer ◽  
Molecular Docking ◽  
Binding Affinity ◽  
Docking Studies ◽  
Target Protein ◽  
Solanum Torvum ◽  
Ms Analysis ◽  
Pharmacokinetic Properties ◽  
Synthetic Drug ◽  
Unripe Fruits

Abstract This study was designed to identify phytocompounds from the aqueous extract of Solanum torvum unripe fruits using GC–MS analysis against breast cancer. For this, the identified phytocompounds were subjected to perform molecular docking studies to find the effects on breast cancer target protein. Pharmacokinetic properties were also tested for the identified phytocompounds to evaluate the ADMET properties. Molecular docking studies were done using docking software PyRx, and pharmacokinetic properties of phytocompounds were evaluated using SwissADME. From the results, ten best compounds were identified from GC–MS analysis against breast cancer target protein. Of which, three compounds showed very good binding affinity with breast cancer target protein. They are ergost-25-ene-3,6-dione,5,12-dihydroxy-,(5.alpha.,12.beta.) (− 7.3 kcal/mol), aspidospermidin-17-ol,1-acetyl-16-methoxy (− 6.7 kcal/mol) and 2-(3,4-dichlorophenyl)-4-[[2-[1-methyl-2-pyrrolidinyl]ethyl amino]-6-[trichloromethyl]-s-triazine (− 6.7 kcal/mol). Further, docking study was performed for the synthetic drug doxorubicin to compare the efficiency of phytocompounds. The binding affinity of ergost-25-ene-3,6-dione,5,12-dihydroxy-,(5.alpha.,12.beta.) is higher than the synthetic drug doxorubicin (− 7.2 kcal/mol), and the binding affinity of other compounds is also very near to the drug. Hence, the present study concludes that the phytocompounds from the aqueous extract of Solanum torvum unripe fruits have the potential ability to treat breast cancer.

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