scholarly journals Spirulina platensis’s phycocyanobilin as an antiangiogenesis by inhibiting VEGFR2-VEGFA pathway in breast cancer: in silico study

JSMARTech ◽  
2021 ◽  
Vol 2 (3) ◽  
pp. 87-91
Author(s):  
Dewa Ayu Putu Ismartati Sukma Jayanti ◽  
◽  
I Gede Agni Abimanyu ◽  
Haidar Azzamudin ◽  
◽  
...  
Keyword(s):  
Breast Cancer ◽  
In Silico ◽  
Spirulina Platensis ◽  
Primary Tumour ◽  
In Silico Analysis ◽  
Data Bank ◽  
Cancer Type ◽  
Ligand Complex ◽  
Discovery Studio ◽  
Angiogenesis Process

Breast cancer is a cancer type that leads to many women deaths. The causes are from the primary tumour and other progressions such as metastatic and angiogenesis. Some therapy strategies have been developed to treat breast cancer, but they are not good enough for treating breast cancer progressions. Spirulina platensis has a phycocyanin and a phycocyanobilin, known as antioxidant and antiinflammatory bioactivities. This study identified anticancer activity of phycocyanobilin from Spirulina platensis. We also investigated the phycocyanobilin mechanism in breast cancer inhibition through VEGFR2-VEGFA pathway. In silico analysis was conducted the inhibition modelling of phycocyanobilin to the VEGF-VEGFR pathway. The VEGF and VEGFR proteins were taken out from Protein Data Bank (PDB) database and were prepared with BIOVIA Discovery Studio 2019. Phycocyanobilin as a ligand was obtained from PubChem and prepared with PyRx. The molecular docking was conducted using HEX 8.0.0 CUDA and the last step is the protein-ligand complexes were visualized and analyzed using BIOVIA Discovery Studio 2019. It results in five protein-ligand complexes in which the receptor-ligand complex VEGFR2-[VEGFA-phycocyanobilin] can inhibit the angiogenesis process by phycocyanobilin binds to VEGFA, and it prevents the angiogenesis process by blocks the VEGFR2 and stops VEGFA to bind with VEGFR2. Thus phycocyanobilin has potential as an anticancer agent especially in breast cancer as an antiangiogenesis.

scholarly journals The Expression of miR-513c and miR-3163 was Downregulated in Tumor Tissues Compared with Margin Tissues of Patients With Breast Cancer

2020 ◽  
Author(s):  
Soheila Delgir ◽  
Khandan Ilkhani ◽  
Asma Safi ◽  
Farhad Seif ◽  
Milad Bastami ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Family History ◽  
In Silico ◽  
In Silico Analysis ◽  
Glutamine Metabolism ◽  
Expression Level ◽  
P Value ◽  
Biological Processes ◽  
Tumor Tissues ◽  
Silico Analysis

Abstract Background Breast cancer (BC) is the most common invasive cancer with different subtypes that its metabolism is unique compared with normal cells. Glutamine is considered a critical nutrition for tumor cell growth and therefore, targeting glutamine metabolism, especially Glutaminase, which catalyzed the conversion of glutamine to glutamate can be beneficial to design anti-cancer agents. Recently, evidence has shown that miRNAs with short length and single strand properties play a significant role in regulating the genes related to glutamine metabolism and may control the development of cancer.Methods Since, in-silico analysis confirmed that miR-513c and miR-3163 might be involved in glutamine metabolism, the expression level of these two miRNAs was evaluated in eighty BC tissues and margin tissues. The data were analyzed to evaluate the correlation between expression level of these miRNAs and patient’s characteristics such as abortion history, family history, and age. Furthermore, in-silico analysis was applied to predict the potential biological processes and molecular pathways of miR-513c and miR-3163 based on its gene targets.Results In-silico studies revealed the top categories of biological processes and pathways that play a critical role in cancer development were target genes for miR-513c and miR-3163. The current study showed that miR-513c (P-value = 0.02062 and fold change= -2.3801) and miR-3163 (P-value = 0.02034 and fold change= -2.3792) were downregulated in tumor tissues compared to margin tissues. Furthermore, the subgroup studies did not show any substantial relationship between expression levels of these two miRNAs and factors such as age, family history cancer, and abortion.Conclusion Based on our data, miR-513c and miR-3163 may be offered as a potential diagnosis and therapeutic targets for patients with BC.

The pharmacoepigenetics of drug metabolism and transport in breast cancer: review of the literature and in silico analysis

2016 ◽  
Vol 17 (14) ◽  
pp. 1573-1585 ◽  
Author(s):  
Rihab Nasr ◽  
Fatima Sleiman ◽  
Zeinab Awada ◽  
Natalie K Zgheib
Keyword(s):  
Breast Cancer ◽  
Drug Metabolism ◽  
In Silico ◽  
In Silico Analysis ◽  
Review Of The Literature ◽  
Cancer Review ◽  
Silico Analysis

In vitro evaluation and molecular dynamics, DFT guided investigation of antimalarial activity of ethnomedicinally used Coptis teeta Wall

2021 ◽  
Vol 24 ◽  
Author(s):  
Ashis Kumar Goswami ◽  
Hemanta Kumar Sharma ◽  
Neelutpal Gogoi ◽  
Ankita Kashyap ◽  
Bhaskar Jyoti Gogoi
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Density Functional ◽  
Antimalarial Activity ◽  
In Silico Analysis ◽  
Dynamics Simulation ◽  
Discovery Studio ◽  
North East ◽  
Silico Analysis

Background: Malaria is caused by different species of Plasmodium; among which P. falciparum is the most severe. Coptis teeta is an ethnomedicinal plant of enormous importance for tribes of north east India. Objective: In this study, the anti malarial activity of the methanol extracts of Coptis teeta was evaluated in vitro and lead identification via in silico study. Method: On the basis of the in vitro results, in silico analysis by application of different modules of Discovery Studio 2018 was performed on multiple targets of P. falciparum taking into consideration some of the compounds reported from C. teeta. Results: The IC50 of the methanol extract of Coptis teeta 0.08 µg/ml in 3D7 strain and 0.7 µg/ml in Dd2 strain of P. falciparum. From the docking study, noroxyhydrastatine was observed to have better binding affinity in comparison to chloroquine. The binding of noroxyhydrastinine with dihydroorotate dehydrogenase was further validated by molecular dynamics simulation and was observed to be significantly stable in comparison to the co-crystal inhibitor. During simulations it was observed that noroxyhydrastinine retained the interactions, giving strong indications of its effectiveness against the P. falciparum proteins and stability in the binding pocket. From the Density-functional theory analysis, the band gap energy of noroxyhydrastinine was found to be 0.186 Ha indicating a favourable interaction. Conclusion: The in silico analysis as an addition to the in vitro results provide strong evidence of noroxyhydrastinine as an anti malarial agent.

scholarly journals Association between SPARC mRNA Expression, Prognosis and Response to Neoadjuvant Chemotherapy in Early Breast Cancer: A Pooled in-silico Analysis

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e62451 ◽  
Author(s):  
Hatem A. Azim ◽  
Sandeep Singhal ◽  
Michail Ignatiadis ◽  
Christine Desmedt ◽  
Debora Fumagalli ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Neoadjuvant Chemotherapy ◽  
Mrna Expression ◽  
Early Breast Cancer ◽  
In Silico ◽  
In Silico Analysis ◽  
Silico Analysis ◽  
Response To Neoadjuvant Chemotherapy

scholarly journals In Silico Analysis Guides Selection of BET Inhibitors for Triple-Negative Breast Cancer Treatment

2016 ◽  
Vol 15 (8) ◽  
pp. 1823-1833 ◽  
Author(s):  
Javier Pérez-Peña ◽  
Gemma Serrano-Heras ◽  
Juan Carlos Montero ◽  
Verónica Corrales-Sánchez ◽  
Atanasio Pandiella ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cancer Treatment ◽  
Triple Negative Breast Cancer ◽  
In Silico ◽  
Triple Negative ◽  
In Silico Analysis ◽  
Breast Cancer Treatment ◽  
Bet Inhibitors ◽  
Silico Analysis ◽  
Selection Of

scholarly journals In vitro and in silico Analysis to Identify Novel Lead Compound from Morinda tinctoria fruit Against Breast Cancer

2019 ◽  
Vol 81 (5) ◽  
Author(s):  
A. Praveena ◽  
S. Arthi ◽  
B. Sudarmathi
Keyword(s):  
Breast Cancer ◽  
In Silico ◽  
In Silico Analysis ◽  
Lead Compound ◽  
Silico Analysis ◽  
Morinda Tinctoria

scholarly journals The POTENTIAL OF BUTTERFLY PEA FLOWER METHANOL EXTRACT AS AN ANTIOXIDANT BY IN SILICO

2020 ◽  
Vol 1 (3) ◽  
pp. 163-169
Author(s):  
Tiana Fitrilia ◽  
M. Fakih Kurniawan ◽  
Febryana Rahayu Kurniawati ◽  
Tirta Setiawan
Keyword(s):  
Nadph Oxidase ◽  
In Silico ◽  
Methanol Extract ◽  
Data Bank ◽  
Computational Method ◽  
Flowering Plant ◽  
Chemical Components ◽  
Discovery Studio ◽  
Butterfly Pea ◽  
G Value

Abstract: Butterfly pea flower (Clitoria ternatea L.) is a flowering plant from the Fabecea family that can grow vines. Butterfly pea flower are known to have chemical components that can act as antioxidants. This study aims to predict the potential of active compounds from methanol extract of butterfly pea flower in inhibiting reactive oxygen species (ROS) based on bond affinity (∆G), the value of Root Mean Square Deviation (RMSD) and their interactions. The method used was a computational method with in silico technique. The software used was Autodock Vina with visualization using the Biovia Discovery Studio Visualizer 2020. The enzyme receptor was NADPH Oxidase (NOX) obtained from Protein Data Bank and the test ligands were a chemical compound from methanol extract of butterfly pea flower. The results of the in silico study showed that the NO had a innate ligand, namely the GTP ligand which has a ∆G value of -7.3 kcal/mol, an RMSD value of 3.1111 Å and the interaction with the receptor that involves the presence of hydrogen bonds. Based on the results of the analysis of 11 test ligands, the chemical component of caffeine was predicted to have the most potential in inhibiting ROS compounds with a value of ∆G -5.4, RMSD value of 1.328 Å and had the same amino acid residue in hydrogen bonding, namely ASP118, and GLY15. The test ligand had the ability to inhibit ROS compounds with a lower level of stability than the innate ligand. Keywords: antioxidant; butterfly pea flower; in silico; NADPH oxidase, ROS

scholarly journals BRCA1 and BRCA2 mutations in breast and ovarian cancer families from south west Colombia

2020 ◽  
pp. 163-175
Author(s):  
Laura Cifuentes-C ◽  
Ana Lucia Rivera-Herrera ◽  
Guillermo Barreto
Keyword(s):  
Breast Cancer ◽  
Ovarian Cancer ◽  
In Silico ◽  
Novel Mutation ◽  
In Silico Analysis ◽  
Moderate Increase ◽  
Brca1 And Brca2 ◽  
Variants Of Uncertain Significance ◽  
Uncertain Significance ◽  
Colombian Pacific

Introduction: Breast cancer is the most common neoplasia of women from all over the world especially women from Colombia. 5%­10% of all cases are caused by hereditary factors, 25% of those cases have mutations in the BRCA1/BRCA2 genes. Objective: The purpose of this study was to identify the mutations associated with the risk of familial breast and/or ovarian cancer in a population of Colombian pacific. Methods: 58 high-risk breast and/or ovarian cancer families and 20 controls were screened for germline mutations in BRCA1 and BRCA2, by Single Strand Conformation Polymorphism (SSCP) and sequencing. Results: Four families (6.9%) were found to carry BRCA1 mutations and eight families (13.8%) had mutations in BRCA2. In BRCA1, we found three Variants of Uncertain Significance (VUS), of which we concluded, using in silico tools, that c.81­12C>G and c.3119G>A (p.Ser1040Asn) are probably deleterious, and c.3083G>A (p.Arg1028His) is probably neutral. In BRCA2, we found three variants of uncertain significance: two were previously described and one novel mutation. Using in silico analysis, we concluded that c.865A>G (p.Asn289Asp) and c.6427T>C (p.Ser2143Pro) are probably deleterious and c.125A>G (p.Tyr42Cys) is probably neutral. Only one of them has previously been reported in Colombia. We also identified 13 polymorphisms (4 in BRCA1 and 9 in BRCA2), two of them are associated with a moderate increase in breast cancer risk (BRCA2 c.1114A>C and c.8755­66T>C). Conclusion: According to our results, the Colombian pacific population presents diverse mutational spectrum for BRCA genes that differs from the findings in other regions in the country.

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