scholarly journals Unravelling Vitamins as Wonder Molecules for Covid-19 Management via Structure-based Virtual Screening

2021 ◽  
Author(s):  
Medha Pandya ◽  
Sejal Shah ◽  
Dhanalakshmi Menamadathil ◽  
Ayushman Gadnayak ◽  
Tanzil Juneja ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Vitamin B12 ◽  
In Silico Analysis ◽  
Host Protein ◽  
Therapeutic Management ◽  
Clinical Settings ◽  
Preparedness Planning ◽  
Vitamin B9 ◽  
Silico Analysis

Abstract The emergence situation of coronavirus disease 2019 (COVID-19) pandemic has realised the global scientific communities to develop strategies for immediate priorities and long-term approaches for utilization of existing knowledge and resources which can be diverted to pandemic preparedness planning. Lack of proper vaccine candidate and therapeutic management has accelerated the researchers to repurpose the existing drugs with known preclinical and toxicity profiles, which can easily enter Phase 3 or 4 or can be used directly in clinical settings. We focused to justify even exploration of supplements, nutrients and vitamins to dampen the disease burden of the current pandemic may play a crucial role for its management. We have explored structure based virtual screening of 15 vitamins against non-structural (NSP3, NSP5, ORF7a, NSP12, ORF3a), structural (Spike & Hemagglutinin esterase) and host protein furin. The in silico analysis exhibited that vitamin B12, Vitamin B9, Vitamin D3 determined suitable binding while vitamin B15 manifested remarkable H-bond interactions with all targets. Vitamin B12 bestowed the lowest energies with human furin and SARS-COV-2 RNA dependent RNA polymerase. Furin mediated cleavage of the viral spike glycoprotein is directly related to enhanced virulence of SARS-CoV-2. In contrast to these, vitamin B12 showed zero affinity with SARS-CoV-2 spike protein. These upshots intimate that Vitamin B12 could be the wonder molecule to shrink the virulence by hindering the furin mediated entry of spike to host cell. These identified molecules may effectively assist in SARS-CoV-2 therapeutic management to boost the immunity by inhibiting the virus imparting relief in lung inflammation.

Enalos Suite of Tools: Enhancing Cheminformatics and Nanoinfor - matics through KNIME

2020 ◽  
Vol 27 (38) ◽  
pp. 6523-6535 ◽  
Author(s):  
Antreas Afantitis ◽  
Andreas Tsoumanis ◽  
Georgia Melagraki
Keyword(s):  
Data Analysis ◽  
Virtual Screening ◽  
In Silico ◽  
Model Development ◽  
In Silico Analysis ◽  
Material Design ◽  
Efficient Solutions ◽  
Biological Data ◽  
Cost Efficient ◽  
Silico Analysis

Drug discovery as well as (nano)material design projects demand the in silico analysis of large datasets of compounds with their corresponding properties/activities, as well as the retrieval and virtual screening of more structures in an effort to identify new potent hits. This is a demanding procedure for which various tools must be combined with different input and output formats. To automate the data analysis required we have developed the necessary tools to facilitate a variety of important tasks to construct workflows that will simplify the handling, processing and modeling of cheminformatics data and will provide time and cost efficient solutions, reproducible and easier to maintain. We therefore develop and present a toolbox of >25 processing modules, Enalos+ nodes, that provide very useful operations within KNIME platform for users interested in the nanoinformatics and cheminformatics analysis of chemical and biological data. With a user-friendly interface, Enalos+ Nodes provide a broad range of important functionalities including data mining and retrieval from large available databases and tools for robust and predictive model development and validation. Enalos+ Nodes are available through KNIME as add-ins and offer valuable tools for extracting useful information and analyzing experimental and virtual screening results in a chem- or nano- informatics framework. On top of that, in an effort to: (i) allow big data analysis through Enalos+ KNIME nodes, (ii) accelerate time demanding computations performed within Enalos+ KNIME nodes and (iii) propose new time and cost efficient nodes integrated within Enalos+ toolbox we have investigated and verified the advantage of GPU calculations within the Enalos+ nodes. Demonstration data sets, tutorial and educational videos allow the user to easily apprehend the functions of the nodes that can be applied for in silico analysis of data.

Using soybean pedigrees to identify genomic selection signatures associated with long-term breeding for cultivar improvement

2018 ◽  
Vol 98 (5) ◽  
pp. 1176-1187 ◽  
Author(s):  
Christopher M. Grainger ◽  
Jocelyne Letarte ◽  
Istvan Rajcan
Keyword(s):  
In Silico Analysis ◽  
Selection Signatures ◽  
Selection Signature ◽  
Breeding Lines ◽  
Genomic Regions ◽  
Elite Breeding Lines ◽  
Silico Analysis ◽  
Simple Sequence ◽  
Introgressive Breeding

Genetic hitchhiking methods used to uncover selection signatures related to traits of agronomic importance in crops have primarily been used at the level of domestication by comparing groups of wild germplasm to landraces or elite breeding lines. In this study, two groups of cultivars defined by an elite Canadian soybean cultivar, ‘OAC Bayfield’, were compared to identify selection signatures related to long-term breeding within a specific region. Cultivars were assigned to either a pre- or post-OAC Bayfield group. Of the 162 simple sequence repeat markers used to genotype members of the pedigree, 14 were fixed and 19 exhibited a selective signature. An in silico analysis compared the results in this study to quantitative trait loci (QTL) reported in SoyBase and showed that 18 out of the 19 markers with a selective signature were associated with at least one QTL. From the 80 QTL associated with the 18 markers, half were related to plant architecture, yield, or maturity. In addition, the number and type of QTL associated with the fixed versus selected loci differed, particularly for yield. Genomic regions exhibiting a selection signature may contain important loci that either need to be conserved for agronomic performance or be targeted for introgressive breeding and germplasm enrichment.

scholarly journals MBRS-13. MiR-1253 POTENTIATES CISPLATIN RESPONSE IN PEDIATRIC MEDULLOBLASTOMA BY REGULATING FERROPTOSIS

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii400-iii400
Author(s):  
Ranjana K Kanchan ◽  
Naveenkumar Perumal ◽  
Pranita Atri ◽  
Ramakanth Chirravuri Venkata ◽  
Ishwor Thapa ◽  
...  
Keyword(s):  
High Risk ◽  
Cell Lines ◽  
In Silico Analysis ◽  
Poor Overall Survival ◽  
Cancer Cell Death ◽  
Pediatric Medulloblastoma ◽  
Mitochondrial Ros ◽  
Group 3 ◽  
Silico Analysis

Abstract Despite improvements in targeted therapies, few group 3 medulloblastoma patients survive long-term. Haploinsufficiency of 17p13.3 is a hallmark of these high-risk tumors; included within this locus is miR-1253, which has tumor suppressive properties in medulloblastoma. Therapeutic strategies capitalizing on the anti-neoplastic properties of miRNAs can provide promising adjuncts to chemotherapy. In this study, we explored the potentiation of miR-1253 on cisplatin cytotoxicity in group 3 MB. Overexpression of miR-1253 sensitized group 3 MB cell lines to cisplatin, leading to a pronounced downregulation in cell viability and induction of apoptosis. Cisplatin is reported as an inducer of both apoptosis and ferroptosis-mediated cancer cell death. In silico analysis revealed an upregulation of several ABC transporters in high-risk MB tumors. When compared to cell lines overexpressing miR-1253, the ABC transporter ABCB7, which regulates both apoptosis and ferroptosis, was revealed as a putative target of miR-1253 with poor survival that may facilitate its chemosensitizing effects by modulating mitochondrial ROS and HIF1α-driven NFκB signaling. We observed high expression of ABCB7 and GPX4, ferroptosis regulators, in MB patients with poor overall survival. MiR-1253 negatively regulated the expression of ABCB7 in Group 3 MB cell lines and induced cytoplasmic ROS and mitochondrial O2-, suggesting ROS-mediated induction of ferroptosis through regulation of ABCB7 and GPX4. Treatment with ROS and ferroptosis inhibitors rescued miR-1253 transfected cells treated with cisplatin. We conclude that miR-1253 induced ROS and potentiated the ferroptotic effects of cisplatin via targeting miR-1253/ABCB7/GPX4/mtROS axis.

scholarly journals VIRTUAL SCREENING OF STILBENE ANALOGUE AND INSILICO, IN VITRO ANTIPROTOZOAL EVALUATION OF LEAD MOLECULES

2017 ◽  
pp. 97-99
Author(s):  
G. Lalasa ◽  
S. Vijayaraj ◽  
K. Thamizhvanan ◽  
K. Chaithanyaveena
Keyword(s):  
Virtual Screening ◽  
In Silico ◽  
In Silico Analysis ◽  
Binding Energies ◽  
Antiprotozoal Activity ◽  
In Vitro Evaluation ◽  
Stilbene Analogues ◽  
Silico Analysis ◽  
Arginase I

Objective: The objective of present study is the virtual screening of stilbene analogues followed by the in silico and in vitro evaluation for its anti protozoal activity.Methods: The method of virtual screening selected is the structure-based virtual screening using ChEMBL database. The in silico analysis was performed using auto dock tools 4.2. The docking was performed using 1T5F (Arginase I-OH complex) as the binding proteins which are drawn from the protein data bank.Results: The stilbene analogues from virtual screening are allowed to dock with the proteins the binding energies and docking positions were determined using auto dock tools 4.2. The in vitro evaluation of anti protozoal activity was performed.Conclusion: The stilbene analogues are capable of producing the antiprotozoal activity.

A systematic review with in silico analysis on transcriptomic profile of gallbladder carcinoma

2020 ◽  
Vol 47 (6) ◽  
pp. 398-408
Author(s):  
Sonam Tulsyan ◽  
Showket Hussain ◽  
Balraj Mittal ◽  
Sundeep Singh Saluja ◽  
Pranay Tanwar ◽  
...  
Keyword(s):  
Systematic Review ◽  
Gallbladder Carcinoma ◽  
In Silico ◽  
In Silico Analysis ◽  
Transcriptomic Profile ◽  
Silico Analysis
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