scholarly journals BioSearch Engine Design : R Code elucidation into the mechanics of search engine that reveals unexplored/untested combinatorial biological hypotheses in silico, using ETC-1922159 data

2018 ◽  
Author(s):  
shriprakash sinha
Keyword(s):  
Colorectal Cancer ◽  
Search Engine ◽  
In Silico ◽  
Expert Advice ◽  
Advice Literature ◽  
Engine Design ◽  
Wnt Inhibitor ◽  
Inhibitor Drug

Often, in biology, we are faced with the problem of exploring relevant unknown biological hypotheses in the form of myriads of combination of factors that might be affecting the pathway under certain conditions. Currently, a major persisting problem is to cherry pick the combinations based on expert advice, literature survey or guesses for investigation. This entails investment in time, energy and expenses at various levels of research. To address these issues, a search engine design was recently been developed, which showed promise by revealing existing con- firmatory published wet lab results. Additionally and of import, the engine mined up a range of unexplored/untested/unknown combinations of genetic factors in the Wnt pathway that were af- fected by ETC-1922159 enantiomer, a PORCN-WNT inhibitor, after the colorectal cancer cells were treated with the inhibitor drug. As an example, MYC is known to upregulate PRC2 com- plex. PRC2 complex contains EZH2, which suppresses tumor suppressor genes via epigenetic modifications. MYC and HOXB8 are up regulated in colorectal cancer, however, the dual working mechanism of the same is not known. The in silico engine showed positioning which correctly approximates and assigns to this 3rd order combination of MYC-HOXB8-EZH2, pointing to the in vitro/in vivo down regulation by ETC-1922159. If the protein interaction of MYC-HOXB8 can be established and a study be done apropos EZH2, it will establish at in vitro/in vivo level, the in silico ranking also. The potential of this engine is immense given the problem faced in biology and other fields. Here we elucidate the R code to understand the mechanics of the search engine in a fluid manner for systems biologists. Though the search engine is in the developmental stage, we share the detailed mechanism of the working principles of the same as it can be generalized to problems in other fields.

scholarly journals BioSearch Engine Design : R Code elucidation into the mechanics of search engine that reveals unexplored/ untested combinatorial biological hypotheses in silico, using ETC-1922159 data.†

2018 ◽  
Author(s):  
Shriprakash Sinha
Keyword(s):  
Colorectal Cancer ◽  
Search Engine ◽  
In Silico ◽  
Expert Advice ◽  
Advice Literature ◽  
Engine Design ◽  
Wnt Inhibitor ◽  
Inhibitor Drug

Often, in biology, we are faced with the problem of exploring relevant unknown biological hypotheses in the form of myriads of combination of factors that might be affecting the pathway under certain conditions. Currently, a major persisting problem is to cherry pick the combinations based on expert advice, literature survey or guesses for investigation. This entails investment in time, energy and expenses at various levels of research. To address these issues, a search engine design was recently been developed, which showed promise by revealing existing confirmatory published wet lab results. Additionally and of import, the engine mined up a range of unexplored/untested/unknown combinations of genetic factors in the Wnt pathway that were affected by ETC-1922159 enantiomer, a PORCN-WNT inhibitor, after the colorectal cancer cells were treated with the inhibitor drug. As an example, MYC is known to upregulate PRC2 complex. PRC2 complex contains EZH2, which suppresses tumor suppressor genes via epigenetic modifications. MYC and HOXB8 are up regulated in colorectal cancer, however, the dual working mechanism of the same is not known. The in silico engine showed positioning which correctly approximates and assigns to this 3rd order combination of MYC-HOXB8-EZH2, pointing to the in vitro/in vivo down regulation by ETC-1922159. If the protein interaction of MYC-HOXB8 can be established and a study be done apropos EZH2, it will establish at in vitro/in vivo level, the in silico ranking also. The potential of this engine is immense given the problem faced in biology and other fields. Here we elucidate the R code to understand the mechanics of the search engine in a fluid manner for systems biologists. Though the search engine is in the developmental stage, we share the detailed mechanism of the working principles of the same as it can be generalizedto problems in other fields.

scholarly journals Inchoative discovery of plausible (un)explored synergistic combinatorial biological hypotheses for static/time series Wnt measurements via ranking search engine : BioSearch Engine Design

2018 ◽  
Author(s):  
shriprakash sinha
Keyword(s):  
Search Engine ◽  
Expert Advice ◽  
Support Vector ◽  
Advice Literature ◽  
Time Investment ◽  
Sensitivity Indices ◽  
Engine Design ◽  
Wnt Inhibitor ◽  
Wet Lab ◽  
Time Buffer

BACKGROUND Often, in biology, we are faced with the problem of exploring relevant unknown biological hypotheses in the form of myriads of combination of factors that might be affecting the pathway under certain conditions. Currently, a major problem in biology is to cherry pick the combinations based on expert advice, literature survey or guesses for investigation. The search and wet lab testing of these combinations costs a lot in terms of time, investment and energy. In a recent development of the PORCN-WNT inhibitor ETC-1922159 for colorectal cancer, a list of down-regulated genes were recorded in a time buffer after the administration of the drug. The regulation of the genes were recorded individually but for a majority, it is still not known which higher (≥ 2) order combinations might be playing a greater role in the pathway. RESULTS The pipeline provides a prioritised list of important 2nd order combinations of a range of family of genes involved in the Wnt pathway. More specifically, it reveals the various unexplored FZD-WNT combinations that have been untested till now in the pathway. In relation to ETC-1922159 affected combinations, the down-regulation of LGR-RNF family after the drug treatment is evident in these rankings as it takes bottom priorities for LGR5-RNF43 combination. The LGR6-RNF43 takes higher ranking than LGR5-RNF43, indicating that it might not be playing a greater role as LGR5 during the Wnt enhancing signals. These rankings confirm the efficacy of the proposed search engine design. CONCLUSION A pipeline has been developed to prioritise an nth order combination of factors that affect a signaling pathway. It takes into account the sensitivity indices computed from variance based (SOBOL) and density-kernel based (HSIC) methods to estimate the influence of each factor or combination of factors. These are then fed as feature vectors into a powerful support vector ranking algorithm that produces a ranked list of the interactions/combinations.

scholarly journals Inchoative Discovery of Plausible (Un)explored Synergistic Combinatorial Biological Hypotheses for Static/Time Series Wnt Measurements via Ranking Search Engine : BioSearch Engine Design

2018 ◽  
Author(s):  
Shriprakash Sinha
Keyword(s):  
Search Engine ◽  
Expert Advice ◽  
Support Vector ◽  
Advice Literature ◽  
Time Investment ◽  
Sensitivity Indices ◽  
Engine Design ◽  
Wnt Inhibitor ◽  
Wet Lab ◽  
Time Buffer

\textsc{Background} Often, in biology, we are faced with the problem of exploring relevant unknown biological hypotheses in the form of myriads of combination of factors that might be affecting the pathway under certain conditions. Currently, a major problem in biology is to cherry pick the combinations based on expert advice, literature survey or guesses for investigation. The search and wet lab testing of these combinations costs a lot in terms of time, investment and energy. In a recent development of the PORCN-WNT inhibitor ETC-1922159 for colorectal cancer, a list of down-regulated genes were recorded in a time buffer after the administration of the drug. The regulation of the genes were recorded individually but for a majority, it is still not known which higher ($\geq 2$) order combinations might be playing a greater role in the pathway. \textsc{Results} The pipeline provides a prioritised list of important $2^{nd}$ order combinations of a range of family of genes involved in the Wnt pathway. More specifically, it reveals the various unexplored FZD-WNT combinations that have been untested till now in the pathway. In relation to ETC-1922159 affected combinations, the down-regulation of LGR-RNF family after the drug treatment is evident in these rankings as it takes bottom priorities for LGR5-RNF43 combination. The LGR6-RNF43 takes higher ranking than LGR5-RNF43, indicating that it might not be playing a greater role as LGR5 during the Wnt enhancing signals. These rankings confirm the efficacy of the proposed search engine design. \textsc{Conclusion} A pipeline has been developed to prioritise an $n^{th}$ order combination of factors that affect a signaling pathway. It takes into account the sensitivity indices computed from variance based (SOBOL) and density-kernel based (HSIC) methods to estimate the influence of each factor or combination of factors. These are then fed as feature vectors into a powerful support vector ranking algorithm that produces a ranked list of the interactions/combinations.

scholarly journals THE POTENTIAL OF ROBUSTA COFFEE (COFFEA CANEPHORA) AS A COLORECTAL CANCER THERAPY MODALITY: AN IN SILICO STUDY

2021 ◽  
pp. 83-87
Author(s):  
DESSY AGUSTINI ◽  
LEO VERNADESLY ◽  
DELVIANA ◽  
THEODORUS
Keyword(s):  
Colorectal Cancer ◽  
In Silico ◽  
Hydrophobic Interactions ◽  
Binding Energies ◽  
In Vivo Studies ◽  
Discovery Studio ◽  
Robusta Coffee ◽  
In Silico Study

Objectives: This research aims to determine the efficacy of compounds in robusta coffee against colorectal cancer through the inhibition of the T-cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) receptor. Methods: This in silico study has been conducted in computing platform from June to August 2021. The selected test compounds would go through the Lipinski rule screening through the SwissADME website and the compounds that met these regulations would be docked to the TIGIT protein using AutoDock Tools and AutoDock Vina. The interactions with the highest binding energies were visualized using BIOVIA Discovery Studio 2020. The test compounds then underwent a toxicity profile analysis on the admetSAR 2.0 website. Results: All test compounds complied with the Lipinski rule. The molecular docking results showed the highest binding energy in kahweol and cafestol (−8.1 kcal/mol) compared to OMC (−7.9 kcal/mol), chlorogenic acid (−7.8 kcal/mol), caffeic acid (−6.3 kcal/mol), caffeine (−6.1 kcal/mol), trigonelline (−5.3 kcal/mol), HMF (−5.1 kcal/mol), furfuryl alcohol (−4.4 kcal/mol), and 5-fluorouracil as the comparator drug (−5.3 kcal/mol). Kahweol, cafestol, and 5-fluorouracil revealed the hydrophobic interactions and hydrogen bonds with amino acid residues in TIGIT. Kahweol and cafestol unveiled minimal toxicity prediction Conclusion: Kahweol and cafestol demonstrated the best results in inhibiting the TIGIT protein which played a role in colorectal cancer. In vitro and in vivo studies are needed to strengthen the findings of this research.

scholarly journals Andean Berry (Vaccinium meridionale Swartz) Juice in Combination With Aspirin Modulated Apoptotic Signaling in Colon Cancer In Vitro and In Vivo

2021 ◽  
Vol 5 (Supplement_2) ◽  
pp. 261-261
Author(s):  
Sandra Arango-Varela ◽  
Ivan Luzardo ◽  
Maria Maldonado-Celis
Keyword(s):  
Colorectal Cancer ◽  
Colon Cancer ◽  
In Silico ◽  
Aberrant Crypt Foci ◽  
Apoptotic Signaling ◽  
Polyphenolic Composition ◽  
Apoptotic Effects ◽  
The Impact

Abstract Objectives This research aimed to assess the impact of Andean Berry (Vaccinium meridionale Swartz) juice (ABJ) in combination with Aspirin in the apoptotic signaling in colon cancer in vitro and in vivo. We hypothesized that ABJ + Aspirin would produce the most effective anti-proliferative and pro-apoptotic effects in vitro and in vivo. Methods The polyphenolic composition of ABJ was carried out by HPLC-DAD. ABJ (0–30% v/v), Aspirin (0–20 mM), and their mixture were evaluated for their pro-apoptotic effects in human SW480 colorectal cancer cells, followed by human apoptosis proteomic and bioinformatic analysis and in silico docking potential between ABJ components and selected pro-apoptotic targets. For the in vivo assays, colorectal cancer was induced with two injections (separated 1 week each) of azoxymethane (AOM: 15 mg/kg body weight, BW), and treatments were evaluated for its chemopreventive and chemoprotective effects. Hence, 30 male and female Balb/c mice were randomly divided in 5 groups: negative control (basal diet, BD); and four AOM-induced groups: positive control (BD), Aspirin (25 mg/kg BW + BD), ABJ (30% v/v in drinking water ABJ + BD), and ABJ + Aspirin (30% v/v ABJ + 25 mg/kg BW Aspirin + BD). Macroscopic and histopathological parameters were evaluated in vivo. Results The mixture displayed the highest antiproliferative effects (+46%), arrested cell cycle at the G2/M phase, decreased cloning efficiency, but reduced Caspase 3/7 activity, suggesting an alternative apoptotic pathway, compared to untreated SW480 cells. Several pro-apoptotic (cytochrome C, TNFRSF1A, Bax, and Bad) and anti-apoptotic (Hsp70/Hsp32) proteins were decreased. ABJ flavonoids (rutin and kaempferol) exhibited the highest in silico affinity with proteins like TRAILR2 or Catalase. Both chemopreventive and chemoprotective approaches showed similar body/liver weight outcomes, but the mixture displayed the strongest aberrant crypt foci reduction in vivo. The chemopreventive approach was more effective in protecting the colon from AOM. Conclusions Results suggested the potential of ABJ to reduce Aspirin use in the alleviation of colorectal cancer markers in vitro and in vivo, modulating alternate pro-apoptotic signaling. Funding Sources The funding provided by COLCIENCIAS and DGAPA-CTIC-UNAM is appreciated.

scholarly journals Sensitivity analysis based ranking reveals unknown biological hypotheses for down regulated genes in time buffer during administration of PORCN-WNT inhibitor ETC-1922159 in CRC†

2017 ◽  
Author(s):  
Shriprakash Sinha
Keyword(s):  
Colorectal Cancer ◽  
Signaling Pathway ◽  
Search Engine ◽  
Higher Order ◽  
Expert Advice ◽  
Support Vector ◽  
Combinatorial Search ◽  
Wnt Inhibitor ◽  
Wet Lab ◽  
Time Buffer

In a recent development of the PORCN-WNT inhibitor ETC-1922159 for colorectal cancer, a list of down-regulated genes were recorded in a time buffer after the administration of the drug. The regulation of the genes were recorded individually but it is still not known which higher (≥ 2) order interactions might be playing a greater role after the administration of the drug. In order to reveal the priority of these higher order interactions among the down-regulated genes or the likely unknown biological hypotheses, a search engine was developed based on the sensitivity indices of the higher order interactions that were ranked using a support vector ranking algorithm and sorted. For example, LGR family (Wnt signal enhancer) is known to neutralize RNF43 (Wnt inhibitor). After the administration of ETC-1922159 it was found that using HSIC (and rbf, linear and laplace variants of kernel) the rankings of the interaction between LGR5-RNF43 were 61, 114 and 85 respectively. Rankings for LGR6-RNF43 were 1652, 939 and 805 respectively. The down-regulation of LGR family after the drug treatment is evident in these rankings as it takes bottom priorities for LGR5-RNF43 interaction. The LGR6-RNF43 takes higher ranking than LGR5-RNF43, indicating that it might not be playing a greater role as LGR5 during the Wnt enhancing signals. These rankings confirm the efficacy of the proposed search engine design. Conclusion: Prioritized unknown biological hypothesis form the basis of further wet lab tests with the aim to reduce the cost of (1) wet lab experiments (2) combinatorial search and (3) lower the testing time for biologist who search for influential interactions in a vast combinatorial search forest. From in silico perspective, a framework for a search engine now exists which can generate rankings for nth order interactions in Wnt signaling pathway, thus revealing unknown/untested/unexplored biological hypotheses and aiding in understanding the mechanism of the pathway. The generic nature of the design can be applied to any signaling pathway or phenomena under investigation where a prioritized order of interactions among the involved factors need to be investigated for deeper understanding. Future improvements of the design are bound to facilitate medical specialists/oncologists in their respective investigations.SignificanceRecent development of PORCN-WNT inhibitor enantiomer ETC-1922159 cancer drug show promise in suppressing some types of colorectal cancer. However, the search and wet lab testing of unknown/unexplored/untested biological hypotheses in the form of combinations of various intra/ extracellular factors/genes/proteins affected by ETC-1922159 is not known. Currently, a major problem in biology is to cherry pick the combinations based on expert advice, literature survey or guesses to investigate a particular combinatorial hypothesis. A search engine has be developed to reveal and prioritise these unknown/untested/unexplored combinations affected by the inhibitor. These ranked unknown biological hypotheses facilitate in narrowing down the investigation in a vast combinatorial search forest of ETC-1922159 affected synergistic-factors.

Phytosomal Curcumin Elicits Anti-tumor Properties Through Suppression of Angiogenesis, Cell Proliferation and Induction of Oxidative Stress in Colorectal Cancer

2019 ◽  
Vol 24 (39) ◽  
pp. 4626-4638 ◽  
Author(s):  
Reyhaneh Moradi-Marjaneh ◽  
Seyed M. Hassanian ◽  
Farzad Rahmani ◽  
Seyed H. Aghaee-Bakhtiari ◽  
Amir Avan ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Colorectal Cancer ◽  
Therapeutic Potential ◽  
Vegf Signaling ◽  
Anticancer Effects ◽  
Inhibition Of Angiogenesis ◽  
Underlying Mechanisms ◽  
Apoptotic Activity

Background: Colorectal cancer (CRC) is one of the most common causes of cancer-associated mortality in the world. Anti-tumor effect of curcumin has been shown in different cancers; however, the therapeutic potential of novel phytosomal curcumin, as well as the underlying molecular mechanism in CRC, has not yet been explored. Methods: The anti-proliferative, anti-migratory and apoptotic activity of phytosomal curcumin in CT26 cells was assessed by MTT assay, wound healing assay and Flow cytometry, respectively. Phytosomal curcumin was also tested for its in-vivo activity in a xenograft mouse model of CRC. In addition, oxidant/antioxidant activity was examined by DCFH-DA assay in vitro, measurement of malondialdehyde (MDA), Thiol and superoxidedismutase (SOD) and catalase (CAT) activity and also evaluation of expression levels of Nrf2 and GCLM by qRT-PCR in tumor tissues. In addition, the effect of phytosomal curcumin on angiogenesis was assessed by the measurement of VEGF-A and VEGFR-1 and VEGF signaling regulatory microRNAs (miRNAs) in tumor tissue. Results: Phytosomal curcumin exerts anti-proliferative, anti-migratory and apoptotic activity in-vitro. It also decreases tumor growth and augmented 5-fluorouracil (5-FU) anti-tumor effect in-vivo. In addition, our data showed that induction of oxidative stress and inhibition of angiogenesis through modulation of VEGF signaling regulatory miRNAs might be underlying mechanisms by which phytosomal curcumin exerted its antitumor effect. Conclusion: Our data confirmed this notion that phytosomal curcumin administrates anticancer effects and can be used as a complementary treatment in clinical settings.

Recent In Vitro and In Silico Advances in the Understanding of Intranasal Drug Delivery

2020 ◽  
Vol 26 ◽  
Author(s):  
John Chen ◽  
Andrew Martin ◽  
Warren H. Finlay
Keyword(s):  
Drug Delivery ◽  
In Silico ◽  
Local Drug Delivery ◽  
In Vivo Studies ◽  
Intranasal Drug Delivery ◽  
Nasal Sprays ◽  
In Silico Studies ◽  
Drug Delivery Devices

Background: Many drugs are delivered intranasally for local or systemic effect, typically in the form of droplets or aerosols. Because of the high cost of in vivo studies, drug developers and researchers often turn to in vitro or in silico testing when first evaluating the behavior and properties of intranasal drug delivery devices and formulations. Recent advances in manufacturing and computer technologies have allowed for increasingly realistic and sophisticated in vitro and in silico reconstructions of the human nasal airways. Objective: To perform a summary of advances in understanding of intranasal drug delivery based on recent in vitro and in silico studies. Conclusion: The turbinates are a common target for local drug delivery applications, and while nasal sprays are able to reach this region, there is currently no broad consensus across the in vitro and in silico literature concerning optimal parameters for device design, formulation properties and patient technique which would maximize turbinate deposition. Nebulizers are able to more easily target the turbinates, but come with the disadvantage of significant lung deposition. Targeting of the olfactory region of the nasal cavity has been explored for potential treatment of central nervous system conditions. Conventional intranasal devices, such as nasal sprays and nebulizers, deliver very little dose to the olfactory region. Recent progress in our understanding of intranasal delivery will be useful in the development of the next generation of intranasal drug delivery devices.

In-silico Studies of Isolated Phytoalkaloid Against Lipoxygenase: Study Based on Possible Correlation

2018 ◽  
Vol 21 (3) ◽  
pp. 215-221
Author(s):  
Haroon Khan ◽  
Muhammad Zafar ◽  
Helena Den-Haan ◽  
Horacio Perez-Sanchez ◽  
Mohammad Amjad Kamal
Keyword(s):  
In Silico ◽  
Docking Studies ◽  
In Vivo Studies ◽  
In Vitro Assays ◽  
Chronic Obstructive ◽  
Lipoxygenase Inhibitors ◽  
Lipoxygenase Inhibition ◽  
In Silico Studies

Aim and Objective: Lipoxygenase (LOX) enzymes play an important role in the pathophysiology of several inflammatory and allergic diseases including bronchial asthma, allergic rhinitis, atopic dermatitis, allergic conjunctivitis, rheumatoid arthritis and chronic obstructive pulmonary disease. Inhibitors of the LOX are believed to be an ideal approach in the treatment of diseases caused by its over-expression. In this regard, several synthetic and natural agents are under investigation worldwide. Alkaloids are the most thoroughly investigated class of natural compounds with outstanding past in clinically useful drugs. In this article, we have discussed various alkaloids of plant origin that have already shown lipoxygenase inhibition in-vitro with possible correlation in in silico studies. Materials and Methods: Molecular docking studies were performed using MOE (Molecular Operating Environment) software. Among the ten reported LOX alkaloids inhibitors, derived from plant, compounds 4, 2, 3 and 1 showed excellent docking scores and receptor sensitivity. Result and Conclusion: These compounds already exhibited in vitro lipoxygenase inhibition and the MOE results strongly correlated with the experimental results. On the basis of these in vitro assays and computer aided results, we suggest that these compounds need further detail in vivo studies and clinical trial for the discovery of new more effective and safe lipoxygenase inhibitors. In conclusion, these results might be useful in the design of new and potential lipoxygenase (LOX) inhibitors.

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