Targeting Melanoma-Initiating Cells by Caffeine: In Silico and In Vitro Approaches

The beneficial effects of coffee on human diseases are well documented, but the molecular mechanisms of its bioactive compounds on cancer are not completely elucidated. This is likely due to the large heterogeneity of coffee preparations and different coffee-based beverages, but also to the choice of experimental models where proliferation, differentiation and immune responses are differently affected. The aim of the present study was to investigate the effects of one of the most interesting bioactive compounds in coffee, i.e., caffeine, using a cellular model of melanoma at a defined differentiation level. A preliminary in silico analysis carried out on public gene-expression databases identified genes potentially involved in caffeine’s effects and suggested some specific molecular targets, including tyrosinase. Proliferation was investigated in vitro on human melanoma initiating cells (MICs) and cytokine expression was measured in conditioned media. Tyrosinase was revealed as a key player in caffeine’s mechanisms of action, suggesting a crucial role in immunomodulation through the reduction in IL-1β, IP-10, MIP-1α, MIP-1β and RANTES secretion onto MICs conditioned media. The potent antiproliferative effects of caffeine on MICs are likely to occur by promoting melanin production and reducing inflammatory signals’ secretion. These data suggest tyrosinase as a key player mediating the effects of caffeine on melanoma.

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Potential Health Benefits Of A Pomegranate Extract, Rich In Phenolic Compounds, In Intestinal Inflammation

Current Nutrition & Food Science ◽

10.2174/1573401317666210222103032 ◽

2021 ◽

Vol 17 ◽

Author(s):

Marco Raffaele ◽

Khaled Greish ◽

Luca Vanella ◽

Giuseppe Carota ◽

Fatemah Bahman ◽

...

Keyword(s):

Bioactive Compounds ◽

Molecular Mechanisms ◽

Intestinal Inflammation ◽

Inflammatory Marker ◽

Experimental Models ◽

Cellular Damage ◽

Experimental Conditions ◽

Potential Health

Background: Pomegranate is a fruit rich in bioactive compounds such as punicalagins, gallic acid, and ellagic acid derivatives. It has been widely used since ancient times in traditional medicine for a wide variety of diseases. It has been reported that bioactive compounds, such as polyphenols, are able to induce the expression of cytoprotective enzymes, including HO-1. The contribution of HO-1 activity to the prevention of intestinal inﬂammation has been shown in different models of Inﬂammatory bowel diseases (IBD). Objective: Aim of the present research was to investigate the molecular mechanisms involved in the beneficial effects of a pomegranate extract (PE), rich in bioactive compounds in intestinal inflammation. Methods: Caco-2 cells exposed to LPS and DSS induced colitis were chosen as convenient experimental models of intestinal inflammation. Results: Results obtained in our experimental conditions, showed that PE in vitro was able to induce HO-1 and to reduce cellular damage and oxidative stress through increase of GSH levels. Moreover, PE was able to decrease the pro-inflammatory marker IL-8 levels and to activate TIGAR pathway. The results obtained in vivo, in agreement with the data obtained in vitro, highlighted the ability of PE to reduce intestinal inflammation, preserve the colon length and histological features and reduce IL-6 levels compared to the DSS treated group. Conclusion: PE, rich in bioactive compounds, could contribute, as supportive therapy, to enhance the effects of the conventional therapeutic strategies to the management of IBD.

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Chemical Profile, Antioxidant and Alpha-Amylase Inhibitory Activity of Leaves Extracts of Annona muricata: A Combined In vitro and In silico Study

Letters in Applied NanoBioScience ◽

10.33263/lianbs112.34703479 ◽

2021 ◽

Vol 11 (2) ◽

pp. 3470-3479

Keyword(s):

Molecular Docking ◽

Inhibitory Activity ◽

In Silico ◽

Molecular Mechanisms ◽

Hydrophobic Interactions ◽

In Silico Analysis ◽

Gas Chromatography Mass Spectrometry ◽

Annona Muricata ◽

Butanol Extract

Leaves of Annona muricata are commonly used for treating diabetes. This study was conducted to investigate the molecular mechanisms involved in the antidiabetic properties of leaves of Annona muricata. Leaves of Annona muricata were extracted separately with H2O, hydromethanol (50% methanol), methanol, ethylacetate, and n-butanol. Chemical characterization of the extracts was performed by spectrophotometry and Gas chromatography-Mass Spectrometry (GC-MS) techniques. Biological activity was determined by α-amylase inhibition assays and molecular docking. The hydromethanol extract had a total phenolics concentration of 117.00±0.59 µg GAE/mg extract whereas; flavonoids were most abundant in the n-butanol extract accounting for 29.34±8.87 µg QE/mg extract. The n-butanol extract had the best FRAP value of 41.17±0.57 Vit C eqv mM, which was significantly higher than the value of the vitamin C reference. Estimated IC50 for all the extracts did not differ significantly but was significantly higher than the reference compound quercetin. All extracts inhibited α-amylase in vitro albeit significantly lower than acarbose. The hydromethanol extract had the highest inhibitory activity (53.31 ± 0.33%). Furthermore, chemical profiling of the hydromethanol extract revealed the presence of a variety of bioactive compounds. In silico analysis by molecular docking of the compounds identified by GC-MS on α-amylase revealed that the compounds had robust molecular interactions orchestrated by H-bonding and hydrophobic interactions. From the results, it can be concluded that extracts of Annona muricata possess antioxidant phytochemicals that inhibit α-amylase. Therefore, the results justify the use of the plant for the treatment of diabetes.

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In Silico and In Vivo Analysis of IL37 in Multiple Sclerosis Reveals Its Probable Homeostatic Role on the Clinical Activity, Disability, and Treatment with Fingolimod

Molecules ◽

10.3390/molecules25010020 ◽

2019 ◽

Vol 25 (1) ◽

pp. 20 ◽

Cited By ~ 6

Author(s):

Eugenio Cavalli ◽

Emanuela Mazzon ◽

Maria Sofia Basile ◽

Santa Mammana ◽

Manuela Pennisi ◽

...

Keyword(s):

Multiple Sclerosis ◽

In Silico ◽

In Silico Analysis ◽

Blood Levels ◽

Clinical Activity ◽

Disease Modifying Drugs ◽

Beneficial Effects ◽

Disease Modifying

We evaluated the in silico expression and circulating levels of interleukin (IL)37 in patients with different forms of multiple sclerosis (MS) and also upon treatment with different disease-modifying drugs. The combined interpretation of the resulting data strengthens and extends the current emerging concept that endogenous IL37 plays an important role in determining onset and progression of MS. The in silico analysis revealed that production of IL37 from cluster of differentiation (CD)4+ T cells from MS patients was reduced in vitro as compared to healthy controls. The analysis of the datasets also demonstrated that “higher” levels of IL37 production from PBMC entailed significant protection from MS relapses. In addition, the in vivo part of the study showed that IL37 was selectively augmented in the sera of MS patients during a relapse and that treatment with the high potency disease-modifying drug fingolimod significantly increased the frequency of patients with circulating blood levels of IL37 (6/9, 66%) as compared to patients receiving no treatment (n = 48) or platform therapy (n = 59) who had levels of IL37 below the limit of the sensitivity of the assay. This finding therefore anticipates that fingolimod may at least partially exert its beneficial effects in MS by upregulating the production of IL37.

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C-C chemokine receptor type 5 links COVID-19, Rheumatoid arthritis, and Hydroxychloroquine: In silico analysis

10.21203/rs.3.rs-48001/v2 ◽

2020 ◽

Author(s):

MAHMOOD Yaseen HACHIM ◽

Ibrahim Hachim ◽

Kashif Naeem ◽

Haifa Hannawi ◽

Issa Al Salmi ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

In Silico ◽

Molecular Mechanisms ◽

Immune Cell ◽

In Silico Analysis ◽

Cell Recruitment ◽

Beneficial Effects ◽

Increased Risk ◽

Patient Groups ◽

Chemotactic Factors

Abstract Patients with rheumatoid arthritis (RA) represent one of the fragile patient groups that might be susceptible to the critical form of the coronavirus disease -19 (COVID-19) . On the other side, RA patients have been found not to have an increased risk of COVID-19 infection. Moreover, some of the Disease-Modifying Anti-Rheumatic Drugs (DMARDS) commonly used to treat rheumatic diseases like Hydroxychloroquine (HCQ) were proposed as a potential therapy for COVID-19 with a lack of full understanding of their molecular mechanisms. This highlights the need for the discovery of common pathways that may link both diseases at the molecular side. In this research, we used the in silico approach to investigate the transcriptomic profile of RA synovium to identify shared molecular pathways with that of severe acute respiratory syndrome-corona virus-2 (SARS-COV-2) infected lung tissue. Our results showed upregulation of chemotactic factors, including CCL4, CCL8, and CCL11, that all shared CCR5 as their receptor, as a common derangement observed in both diseases; RA and COVID-19. Moreover, our results also highlighted a possible mechanism through which HCQ, which can be used as a monotherapy in mild RA or as one of the triple-DMARDs therapy (tDMARDs; methotrexate, sulphasalazine, and HCQ), might interfere with the COVID-19 infection. This might be achieved through the ability of HCQ to upregulate specific immune cell populations like activated natural killer (NK) cells, which were found to be significantly reduced in COVID-19 infection. In addition to its ability to block CCR5 rich immune cell recruitment that also was upregulated in the SARS-COV-2 infected lungs. This might explain some of the reports that showed beneficial effects.

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Thymus musilii Velen. as a promising source of potent bioactive compounds with its pharmacological properties: In vitro and in silico analysis

Arabian Journal of Chemistry ◽

10.1016/j.arabjc.2020.06.032 ◽

2020 ◽

Vol 13 (8) ◽

pp. 6782-6801 ◽

Cited By ~ 3

Author(s):

Khalil Mseddi ◽

Fathi Alimi ◽

Emira Noumi ◽

Vajid N. Veettil ◽

Sumukh Deshpande ◽

...

Keyword(s):

Bioactive Compounds ◽

In Silico ◽

In Silico Analysis ◽

Pharmacological Properties ◽

Promising Source ◽

Silico Analysis

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C-C chemokine receptor type 5 links COVID-19, rheumatoid arthritis, and Hydroxychloroquine: in silico analysis

Translational Medicine Communications ◽

10.1186/s41231-020-00066-x ◽

2020 ◽

Vol 5 (1) ◽

Author(s):

Mahmood Y. Hachim ◽

Ibrahim Y. Hachim ◽

Kashif Bin Naeem ◽

Haifa Hannawi ◽

Issa Al Salmi ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

In Silico ◽

Molecular Mechanisms ◽

Immune Cell ◽

In Silico Analysis ◽

Cell Recruitment ◽

Beneficial Effects ◽

Increased Risk ◽

Patient Groups ◽

Chemotactic Factors

Abstract Patients with rheumatoid arthritis (RA) represent one of the fragile patient groups that might be susceptible to the critical form of the coronavirus disease − 19 (COVID-19). On the other side, RA patients have been found not to have an increased risk of COVID-19 infection. Moreover, some of the Disease-Modifying Anti-Rheumatic Drugs (DMARDS) commonly used to treat rheumatic diseases like Hydroxychloroquine (HCQ) were proposed as a potential therapy for COVID-19 with a lack of full understanding of their molecular mechanisms. This highlights the need for the discovery of common pathways that may link both diseases at the molecular side. In this research, we used the in silico approach to investigate the transcriptomic profile of RA synovium to identify shared molecular pathways with that of severe acute respiratory syndrome-corona virus-2 (SARS-COV-2) infected lung tissue. Our results showed upregulation of chemotactic factors, including CCL4, CCL8, and CCL11, that all shared CCR5 as their receptor, as a common derangement observed in both diseases; RA and COVID-19. Moreover, our results also highlighted a possible mechanism through which HCQ, which can be used as a monotherapy in mild RA or as one of the triple-DMARDs therapy (tDMARDs; methotrexate, sulphasalazine, and HCQ), might interfere with the COVID-19 infection. This might be achieved through the ability of HCQ to upregulate specific immune cell populations like activated natural killer (NK) cells, which were found to be significantly reduced in COVID-19 infection. In addition to its ability to block CCR5 rich immune cell recruitment that also was upregulated in the SARS-COV-2 infected lungs. This might explain some of the reports that showed beneficial effects.

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Anti-atherosclerotic effects of fruit bioactive compounds: A review of current scientific evidence

Canadian Journal of Plant Science ◽

10.4141/cjps2011-090 ◽

2012 ◽

Vol 92 (3) ◽

pp. 407-419 ◽

Cited By ~ 36

Author(s):

Surangi H. Thilakarathna ◽

H. P. Vasantha Rupasinghe

Keyword(s):

Bioactive Compounds ◽

Antioxidant Activities ◽

Scientific Evidence ◽

Experimental Models ◽

Lipid Lowering ◽

Experimental Conditions ◽

Beneficial Effects ◽

Positive Effects

Thilakarathna, S. H. and Rupasinghe, H. P. V. 2012. Anti-atherosclerotic effects of fruit bioactive compounds: A review of current scientific evidence. Can. J. Plant Sci. 92: 407–419. Atherosclerosis is a condition which leads to a cascade of processes involved in thickening of arterial walls as a result of fatty deposition, which can increase the risk of cardiovascular diseases. Among numerous remedies, the consumption of fruits is believed to have beneficial effects on atherosclerosis development. Various bioactive compounds are present in fruits and they have been found to be responsible for exerting these beneficial effects. Fruit flavonoids and certain terpenoids are among the most efficacious fruit bioactive compounds that have shown positive effects on different in vitro as well as in vivo research models of atherosclerosis. The mechanisms of actions of these compounds vary from exerting antioxidant activities to anti-atherogenic and lipid lowering activities, based on different experimental models. This review article briefly explains how some of the fruit bioactive compounds have affected atherosclerosis under experimental conditions.

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Antiproliferative Activity of Stokesia laevis Ethanolic Extract in Combination with Several Food-Related Bioactive Compounds; In Vitro (CaCO2) And in Silico Docking (TNKS1) Studies

10.20944/preprints202109.0475.v1 ◽

2021 ◽

Author(s):

Georgeta Neagu ◽

Amalia Stefaniu ◽

Adrian Albulescu ◽

Lucia Pintilie ◽

Lucia Camelia Pirvu

Keyword(s):

Bioactive Compounds ◽

In Silico ◽

Catalytic Domain ◽

Tumor Cell Line ◽

Ethanolic Extract ◽

Human Colon ◽

Docking Studies ◽

Antiproliferative Effects ◽

In Silico Docking

In this study, five polyphenol compounds (reference substances, ref.) were added to Stokesia laevis (Slae26) ethanolic extract (5 mg GAE / mL) in order to test their antiproliferative effects on human colon tumor cell line Caco-2 (ATCC-HTB-37). The five phenolics (ref.) are luteolin-7-O-glucoside (orientin), luteolin-8-C-glucoside (cinnaroside), caffeic acid, gentisic acid and para-aminobenzoic acid (PABA), and they were combined in ratio 1:1 between the active compounds in samples (GAE : ref.). Results indicated certain antiproliferative effects of Slae26 (IC50=36 μg GAE/mL sample), of the five reference compounds, but mainly of Slae26 combinations with the five phenolics tested (ref.). Punctually, there were obtained IC50 values around 5 μg/mL sample, signifying real therapeutic usefulness and antitumor potency of Slae26 combinations with the five food bioactive compounds tested. In silico docking studies provided potential therapeutic agents to inhibit the catalytic domain of human tankyrase 1 (TNKS1) in the series of food bioactive compounds tested, and revealed luteolin-7-O-glucoside high effectiveness.

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In Silico Study of Potential Cross-Kingdom Plant MicroRNA Based Regulation in Chronic Myeloid Leukemia

Current Pharmacogenomics and Personalized Medicine ◽

10.2174/1875692118666200106113610 ◽

2020 ◽

Vol 17 (2) ◽

pp. 125-132

Author(s):

Marjanu Hikmah Elias ◽

Noraziah Nordin ◽

Nazefah Abdul Hamid

Keyword(s):

Targeted Therapy ◽

In Silico ◽

Structure Prediction ◽

Tertiary Structure ◽

Target Prediction ◽

In Silico Analysis ◽

Microrna Target ◽

Good Target

Background: Chronic Myeloid Leukaemia (CML) is associated with the BCRABL1 gene, which plays a central role in the pathogenesis of CML. Thus, it is crucial to suppress the expression of BCR-ABL1 in the treatment of CML. MicroRNA is known to be a gene expression regulator and is thus a good candidate for molecularly targeted therapy for CML. Objective: This study aims to identify the microRNAs from edible plants targeting the 3’ Untranslated Region (3’UTR) of BCR-ABL1. Methods: In this in silico analysis, the sequence of 3’UTR of BCR-ABL1 was obtained from Ensembl Genome Browser. PsRNATarget Analysis Server and MicroRNA Target Prediction (miRTar) Server were used to identify miRNAs that have binding conformity with 3’UTR of BCR-ABL1. The MiRBase database was used to validate the species of plants expressing the miRNAs. The RNAfold web server and RNA COMPOSER were used for secondary and tertiary structure prediction, respectively. Results: In silico analyses revealed that cpa-miR8154, csi-miR3952, gma-miR4414-5p, mdm-miR482c, osa-miR1858a and osa-miR1858b show binding conformity with strong molecular interaction towards 3’UTR region of BCR-ABL1. However, only cpa-miR- 8154, osa-miR-1858a and osa-miR-1858b showed good target site accessibility. Conclusion: It is predicted that these microRNAs post-transcriptionally inhibit the BCRABL1 gene and thus could be a potential molecular targeted therapy for CML. However, further studies involving in vitro, in vivo and functional analyses need to be carried out to determine the ability of these miRNAs to form the basis for targeted therapy for CML.

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In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

Current Chemical Biology ◽

10.2174/2212796812666180622103906 ◽

2019 ◽

Vol 13 (2) ◽

pp. 159-170 ◽

Cited By ~ 1

Author(s):

Vishal Ahuja ◽

Aashima Sharma ◽

Ranju Kumari Rathour ◽

Vaishali Sharma ◽

Nidhi Rana ◽

...

Keyword(s):

Production Process ◽

In Silico ◽

Xylose Reductase ◽

In Silico Analysis ◽

Emericella Nidulans ◽

Higher Temperature ◽

In Silico Characterization ◽

Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

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