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Article ; Online: Pinpointing top inhibitors for GSK3β from pool of indirubin derivatives using rigorous computational workflow and their validation using molecular dynamics (MD) simulations.

Pandya, Vamangi / Rao, Priyashi / Prajapati, Jignesh / Rawal, Rakesh M / Goswami, Dweipayan

2024 Volume 14, Issue 1, Page(s) 49

Abstract: Glycogen synthase kinase-3β (GSK3β) is a pivotal protein kinase implicated in a spectrum of debilitating diseases, encompassing cancer, diabetes, and neurodegenerative disorders. While the therapeutic potential of GSK3β inhibition is widely recognized, ... ...

Abstract	Glycogen synthase kinase-3β (GSK3β) is a pivotal protein kinase implicated in a spectrum of debilitating diseases, encompassing cancer, diabetes, and neurodegenerative disorders. While the therapeutic potential of GSK3β inhibition is widely recognized, there remains an unmet need for a rigorous, systematic analysis probing the theoretical inhibition dynamics of a comprehensive library of indirubin derivatives against GSK3β using advanced computational methodologies. Addressing this gap, this study embarked on an ambitious endeavor, leveraging indirubin-a renowned scaffold-as a template to curate a vast library of 1000 indirubin derivatives from PubChem. These were enriched with varied substitutions and modifications, identified via a structure similarity search with a Tanimoto similarity threshold of 85%. Harnessing a robust virtual screening workflow, we meticulously identified the top 10 contenders based on XP docking scores. Delving deeper, we gauged the binding free energy differentials (ΔGBind) of these hits, spotlighting the top three compounds that showcased unparalleled binding prowess. A comparative pharmacophore feature mapping with the reference inhibitor OH8, co-crystallized with GSK3β (PDB ID: 6Y9R), was undertaken. The binding dynamics of these elite compounds were further corroborated with 100 ns molecular dynamics simulations, underlining their stable and potent interactions with GSK3β. Remarkably, our findings unveil that these indirubin derivatives not only match but, in certain scenarios, surpass the binding affinity and specificity of OH8. By bridging this research chasm, our study amplifies the therapeutic promise of indirubin derivatives, positioning them as frontrunners in the quest for groundbreaking GSK3β inhibitors, potentially revolutionizing treatments for a myriad of ailments.
MeSH term(s)	Molecular Dynamics Simulation ; Glycogen Synthase Kinase 3 beta ; Workflow ; Indoles/pharmacology ; Molecular Docking Simulation
Chemical Substances	Glycogen Synthase Kinase 3 beta (EC 2.7.11.1) ; indirubin (V86L8P74GI) ; Indoles
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-50992-7
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Article ; Online: Extending the lore of curcumin as dipteran Butyrylcholine esterase (BChE) inhibitor: A holistic molecular interplay assessment.

Rao, Priyashi / Goswami, Dweipayan / Rawal, Rakesh M

PloS one

2022 Volume 17, Issue 5, Page(s) e0269036

Abstract: Since its origin, the emergence of vector-borne infections has taken a toll on incalculable human lives. The use of chemical insecticides is one of the early known methods of vector control and although their use is still a prevalent way to combat insect ...

Abstract	Since its origin, the emergence of vector-borne infections has taken a toll on incalculable human lives. The use of chemical insecticides is one of the early known methods of vector control and although their use is still a prevalent way to combat insect population sadly the perils of insects related transmission still persists. Most commonly, the existing insecticides face the wrath of getting resisted repeatedly, paying way to develop resilient, efficient, and cost-effective natural insecticides. In this study, computational screening was performed using homology modelling, E-pharmacophore feature mapping, molecular docking, Density Function Theory (DFT) assessment, Molecular mechanics generalized Born surface area (MM-GBSA) based binding free energy calculations and Molecular Dynamics (MD) simulation to identify a potential lead phytochemical out of a manually curated library from published literature. The protein target used under this study is insect Butyrylcholine esterase (BChE). Additionally, in vitro insect (Aedes aegypti) BChE inhibition assay was also performed with the top phytochemical identified from in silico assessments. Our research highlights that curcumin leads to inhibition of enzyme BChE of Ae. aegypti. The identified mode of action of curcumin as an insect BChE inhibitor indicates the possibility of its use as an environment friendly and natural futuristic insecticide.
MeSH term(s)	Aedes ; Animals ; Choline/analogs & derivatives ; Cholinesterases/metabolism ; Curcumin/metabolism ; Curcumin/pharmacology ; Enzyme Inhibitors/pharmacology ; Humans ; Insecticide Resistance ; Insecticides/metabolism ; Insecticides/pharmacology ; Molecular Docking Simulation ; Mosquito Vectors/metabolism
Chemical Substances	Enzyme Inhibitors ; Insecticides ; butyrylcholine (3922-86-9) ; Cholinesterases (EC 3.1.1.8) ; Curcumin (IT942ZTH98) ; Choline (N91BDP6H0X)
Language	English
Publishing date	2022-05-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0269036
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Article ; Online: Molecular insights on ar-turmerone as a structural, functional and pharmacophoric analogue of synthetic mosquito repellent DEET by comprehensive computational assessment.

Rao, Priyashi / Goswami, Dweipayan / Rawal, Rakesh M

Scientific reports

2022 Volume 12, Issue 1, Page(s) 15564

Abstract: Mosquitoes are vectors for a variety of infectious illnesses, and chemical synthetic insecticides have made it possible to control them effectively. Mosquito repellents are a typical means of keeping mosquitos at bay. Because of its main effectiveness of ...

Abstract	Mosquitoes are vectors for a variety of infectious illnesses, and chemical synthetic insecticides have made it possible to control them effectively. Mosquito repellents are a typical means of keeping mosquitos at bay. Because of its main effectiveness of skin permeability, N,N-Diethyl-meta-toluamide (DEET) is one of the most extensively used mosquito repellents but a dangerous synthetic chemical. DEET was identified about a decade ago to inhibit mosquito's Odorant Binding Protein 1 (OBP1), impairing the mosquito's ability to recognise the host body odour. OBP1 has been identified as a possible target for the development of new mosquito repellents since its discovery. Essential oils from different plants, on the other hand, have been used to repel mosquitos since antiquity. One essential oil from the Curcuma longa (Zingiberales: Zingiberaceae) rhizome display mosquito repellent properties, according to the literature. Furthermore, one of the phytochemicals found in abundance in C. longa essential oil, ar-turmerone, exhibits mosquito repellency as comparable to synthetic DEET. Till date studies on in-silico interaction of natural ar-turmerone with OBP1, which we depict in our current work are scarce. Further, there exist no published reports demonstrating the literary evidence on detailed insights of interaction of DEET with OBP1 along with Molecular Dynamics (MD) simulation studies. We further performed detailed molecular investigations using pharmacophore analysis of ar-turmerone and compared it with DEET, where our findings in the current manuscript unveils for the first time that ar-turmerone is a functional, structural and pharmacophoric analogue of DEET.
MeSH term(s)	Animals ; DEET/pharmacology ; Insect Repellents/chemistry ; Insect Repellents/pharmacology ; Insecticides ; Ketones ; Oils, Volatile/chemistry ; Oils, Volatile/pharmacology ; Sesquiterpenes
Chemical Substances	Insect Repellents ; Insecticides ; Ketones ; Oils, Volatile ; Sesquiterpenes ; DEET (134-62-3) ; ar-turmerone (1944T899NO)
Language	English
Publishing date	2022-09-16
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-19901-2
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Article ; Online: Curcumin interferes with chitin synthesis in Aedes aegypti: a computational and experimental investigation.

Rao, Priyashi / Ninama, Jinal / Dudhat, Mansi / Goswami, Dweipayan / Rawal, Rakesh M

Molecular diversity

2023

Abstract: Throughout history, vector-borne diseases have consistently posed significant challenges to human health. Among the strategies for vector control, chemical insecticides have seen widespread use since their inception. Nevertheless, their effectiveness is ... ...

Abstract	Throughout history, vector-borne diseases have consistently posed significant challenges to human health. Among the strategies for vector control, chemical insecticides have seen widespread use since their inception. Nevertheless, their effectiveness is continually undermined by the steady growth of insecticide resistance within these vector populations. As such, the demand for more robust, efficient, and cost-effective natural insecticides has become increasingly pressing. One promising avenue of research focuses on chitin, a crucial structural component of mosquitoes' exoskeletons and other insects. Chitin not only provides protection and rigidity but also lends flexibility to the insect body. It undergoes substantial transformations during insect molting, a process known as ecdysis. Crucially, the production of chitin is facilitated by an enzyme known as chitin synthase, making it an attractive target for potential novel insecticides. Our recent study delved into the impacts of curcumin, a natural derivative of turmeric, on chitin synthesis and larval development in Aedes aegypti, a mosquito species known to transmit dengue and yellow fever. Our findings demonstrate that even sub-lethal amounts of curcumin can significantly reduce overall chitin content and disrupt the cuticle development in the 4th instar larvae of Aedes aegypti. Further to this, we utilized computational analyses to investigate how curcumin interacts with chitin synthase. Techniques such as molecular docking, pharmacophore feature mapping, and molecular dynamics (MD) simulations helped to illustrate that curcumin binds to the same site as polyoxin D, a recognized inhibitor of chitin synthase. These findings point to curcumin's potential as a natural, bioactive larvicide that targets chitin synthase in mosquitoes and potentially other insects.
Language	English
Publishing date	2023-06-26
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10672-0
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Article ; Online: Revealing the molecular interplay of curcumin as Culex pipiens Acetylcholine esterase 1 (AChE1) inhibitor.

Rao, Priyashi / Goswami, Dweipayan / Rawal, Rakesh M

Scientific reports

2021 Volume 11, Issue 1, Page(s) 17474

Abstract: Emergence of vector borne diseases has continued to take toll on millions of lives since its inception. The use of insecticides began as vector control strategy in the early 1900's but the menace of insects is still prevalent. Additionally, the ... ...

Abstract	Emergence of vector borne diseases has continued to take toll on millions of lives since its inception. The use of insecticides began as vector control strategy in the early 1900's but the menace of insects is still prevalent. Additionally, the inadequate use of organophosphates and carbamates which target acetylcholine esterase (AChE), are known to develop resistance amongst vectors of transmission and are toxic to humans. In this study, extensive computational screening was performed using homology modelling, molecular docking, molecular dynamics (MD) simulation and free energy change calculation, which highlighted curcumin as a lead molecule out of ~ 1700 phytochemicals against Culex pipiens AChE. In vivo larvicidal activity was carried out along with in vivo and in vitro AChE inhibition assay to determine the biochemical efficacy of curcumin. Our study reveals that curcumin induces mortality in Cx. pipiens at an early stage of its life cycle by AChE inhibition. This also underlines the use of curcumin as a coming-age natural product insecticide.
MeSH term(s)	Acetylcholine/metabolism ; Acetylcholinesterase/chemistry ; Amino Acid Sequence ; Animals ; Cholinesterase Inhibitors/pharmacology ; Culex/enzymology ; Curcumin/pharmacology ; Molecular Docking Simulation ; Protein Conformation ; Sequence Homology
Chemical Substances	Cholinesterase Inhibitors ; Acetylcholinesterase (EC 3.1.1.7) ; Curcumin (IT942ZTH98) ; Acetylcholine (N9YNS0M02X)
Language	English
Publishing date	2021-09-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-96963-8
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Article ; Online: Rapid method for detection, quantification and measuring microbial degradation of pesticide-thiram using high performance thin layer chromatography (HPTLC)

Chouhan, Sonalkunwar / Mulani, Rinkal / Ansari, Hafsa / Sindhav, Gaurang / Rao, Priyashi / Rawal, Rakesh M. / Saraf, Meenu / Goswami, Dweipayan

Environ Sci Pollut Res. 2023 Jan., v. 30, no. 3 p.7874-7885

2023

Abstract: Thiram (tetramethylthiuramdisulfide) or thiram sulphide is a dithiocarbamate group of non-systemic group of fungicide which are applied for seed treatment, control of the crop pests, to repel animals, etc. Moreover, thiram has also been responsible to ... ...

Abstract	Thiram (tetramethylthiuramdisulfide) or thiram sulphide is a dithiocarbamate group of non-systemic group of fungicide which are applied for seed treatment, control of the crop pests, to repel animals, etc. Moreover, thiram has also been responsible to cause moderate skin sensitivity and eye irritation. Higher exposure to thiram might also lead to developmental damages to newborn and neurotoxic effects to non-target organisms. Advancing to prevent such toxic effects and prevention of soil fertility from thiram and thiram-like chemicals is indispensable. The analytical High-Performance Thin-Layer Chromatography (HPTLC) is a simple, quick and a reliable method was proposed and validated for the detection and quantification of various small molecules for many years. This manuscript represents the solution to use microbes to degrade the thiram present in the soil and for that, HPTLC based method to study thiram degradation by Pseudomonas has been designed. Herein, a HPTLC protocol formalised to reveal the detection and quantification of thiram within the range of 100 to 700 ng/spot on TLC plate. The same concentration was then used for calculating percent microbial degradation of thiram from the culture broth. To perform the microbial degradation of thiram, Pseudomonas otitidis strain TD-8 and Pseudomonas stutzeri strain TD-18 were taken as thiram degrader microbial strain. The efficacy of TD-8 to degrade thiram was identified to be 81 and 99% when grown in presence of thiram for 4 days and 8 days, respectively, while TD-18 strain’s efficacy to degrade thiram was found to be 57% and 99% when grown in presence of thiram for 4 days and 8 days, respectively.
Keywords	Pseudomonas stutzeri ; biodegradation ; culture media ; eye irritation ; neonates ; neurotoxicity ; rapid methods ; seed treatment ; soil ; soil fertility ; sulfides ; thin layer chromatography ; thiram
Language	English
Dates of publication	2023-01
Size	p. 7874-7885.
Publishing place	Springer Berlin Heidelberg
Document type	Article ; Online
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-022-22731-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A Comprehensive in vitro and in silico Assessment on Inhibition of CYP51B and Ergosterol Biosynthesis by Eugenol in Rhizopus oryzae

Prajapati, Jignesh / Rao, Priyashi / Poojara, Lipi / Acharya, Dhaval / Patel, Saumya K. / Goswami, Dweipayan / Rawal, Rakesh M.

Curr Microbiol. 2023 Jan., v. 80, no. 1 p.47-47

2023

Abstract: Mucormycosis, also known as Zygomycosis, is a disease caused by invasive fungi, predominantly Rhizopus species belonging to the Order of Mucorales. Seeing from the chemistry perspective, heterocyclic compounds with an "azole" moiety are widely employed ... ...

Abstract	Mucormycosis, also known as Zygomycosis, is a disease caused by invasive fungi, predominantly Rhizopus species belonging to the Order of Mucorales. Seeing from the chemistry perspective, heterocyclic compounds with an "azole" moiety are widely employed as antifungal agent for minimising the effect of mucormycosis as a prescribed treatment. These azoles serve as non-competitive inhibitors of fungal CYP51B by predominantly binding to its heme moiety, rendering its inhibition. However, long-term usage and abuse of azoles as antifungal medicines has resulted in drug resistance among certain fungal pathogens. Hence, there is an unmet need to find alternative therapeutic compounds. In present study, we used various in vitro tests to investigate the antifungal activity of eugenol against R. oryzae/R. arrhizus, including ergosterol quantification to test inhibition of ergosterol production mediated antifungal action. The minimum inhibitory concentration (MIC) value obtained for eugenol was 512 μg/ml with reduced ergosterol concentration of 77.11 ± 3.25% at MIC/2 concentration. Further, the molecular interactions of eugenol with fungal CYP51B were meticulously studied making use of proteomics in silico study including molecular docking and molecular dynamics simulations that showed eugenol to be strongly interacting with heme in an identical fashion to that shown by azole drugs (in this case, clotrimazole was evaluated). This is the first of a kind study showing the simulation study of eugenol with CYP51B of fungi. This inhibition results in ergosterol synthesis and is also studied and compared with keeping clotrimazole as a reference.
Keywords	Rhizopus oryzae ; antifungal properties ; biosynthesis ; clotrimazole ; computer simulation ; drug resistance ; ergosterol ; eugenol ; fungi ; heme ; minimum inhibitory concentration ; moieties ; molecular dynamics ; proteomics ; therapeutics ; zygomycosis
Language	English
Dates of publication	2023-01
Size	p. 47.
Publishing place	Springer US
Document type	Article ; Online
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-022-03108-9
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Article: Perceiving SARS-CoV-2 Mpro and PLpro dual inhibitors from pool of recognized antiviral compounds of endophytic microbes: an in silico simulation study.

Prajapati, Jignesh / Patel, Rohit / Rao, Priyashi / Saraf, Meenu / Rawal, Rakesh / Goswami, Dweipayan

Structural chemistry

2022 Volume 33, Issue 5, Page(s) 1619–1643

Abstract: Coronavirus disease 2019 (COVID-19) persists and shook the global population where the endgame to this pandemic is brought on by developing vaccines in record-breaking time. Nevertheless, these vaccines are far from perfect where their efficiency ranges ... ...

Abstract	Coronavirus disease 2019 (COVID-19) persists and shook the global population where the endgame to this pandemic is brought on by developing vaccines in record-breaking time. Nevertheless, these vaccines are far from perfect where their efficiency ranges from 65 to 90%; therefore, vaccines are not the one only solution to overcome this situation, and apart from administration of vaccines, the scientific community is at quest for finding alternative solutions to incumber SARS-CoV-2 infection. In this study, our research group is keen on identifying a bioactive molecule that is independent in its mode of action from existing vaccines which can potentially target the SARS-CoV-2 virus replicative efficacy. Papain-like protease (PLpro) and main protease (Mpro) are the most lucrative targets of COVIDs against which the drugs can be developed, as these proteases play a vital role in the replication and development of viral particles. Researchers have modelled a compound such as GRL0617 and X77 as an inhibitor of Mpro and PLpro, respectively, but use of these compounds has several limitations on hosts like toxicity and solubility. Under the current study by deploying rigorous computational assessments, pool of microbial secondary metabolites was screened and handpicked to search a structural or functional analogue of GRL0617 and X77, with an idea to identify a compound that can serve as dual inhibitor for both PLpro and Mpro. From the manually curated database of known antiviral compounds from fungal origin, we found cytonic acids A and B to potentially serve as dual inhibitor of PLpro and Mpro.
Language	English
Publishing date	2022-04-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2018832-8
ISSN	1572-9001 ; 1040-0400
ISSN (online)	1572-9001
ISSN	1040-0400
DOI	10.1007/s11224-022-01932-0
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Article ; Online: Identification of hub genes associated with prognosis of lung cancer via integrated bioinformatics and

Yadav, Deep Kumari / Bhadresha, Kinjal / Rao, Priyashi / Shaikh, Shayma / Rawal, Rakesh M

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 20, Page(s) 11204–11218

Abstract: Lung cancer is a severe health problem that affects more men than women around the world. The goal of this study was to identify the biomarker hub genes for lung cancer in order to ascertain the biological pathway and protein- protein interaction ... ...

Abstract	Lung cancer is a severe health problem that affects more men than women around the world. The goal of this study was to identify the biomarker hub genes for lung cancer in order to ascertain the biological pathway and protein- protein interaction networks. The microarray datasets GSE80796, GSE68571, GSE118370 and GSE43458 were retrieved from the GEO database and were analysed using GEO2R. STRING, Cytoscape, and cytoHubba were used to construct the PPI network and hub genes. GEPIA was used to obtain the overall survival and expression level in LUAD/LUSC and normal tissue. The MTT assay was used to examine antiproliferative activity. PI staining was used to determine the cell cycle arrest. qPCR was used to analyse gene expressions. The datasets revealed a total of 401 common DEGs, with 258 up-regulated genes and 143 down-regulated genes. Further,
MeSH term(s)	Male ; Female ; Humans ; Lung Neoplasms/genetics ; Gene Expression Profiling ; Biomarkers, Tumor/genetics ; Computational Biology ; Gallic Acid ; Gene Expression Regulation, Neoplastic
Chemical Substances	Biomarkers, Tumor ; Gallic Acid (632XD903SP)
Language	English
Publishing date	2022-12-26
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2160816
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Article ; Online: Unveiling the nature's fruit basket to computationally identify Citrus sinensis csi-mir169-3p as a probable plant miRNA against Reference and Omicron SARS-CoV-2 genome.

Mangukia, Naman / Rao, Priyashi / Patel, Kamlesh / Pandya, Himanshu / Rawal, Rakesh M

Computers in biology and medicine

2022 Volume 146, Page(s) 105502

Abstract: The fundamental role of microRNAs (miRNAs) has long been associated with regulation of gene expression during transcription and post transcription of mRNA's 3'UTR by the RNA interference mechanism. Also, the process of how miRNAs tend to induce mRNA ... ...

Abstract	The fundamental role of microRNAs (miRNAs) has long been associated with regulation of gene expression during transcription and post transcription of mRNA's 3'UTR by the RNA interference mechanism. Also, the process of how miRNAs tend to induce mRNA degradation has been predominantly studied in many infectious diseases. In this article, we would like to discuss the interaction of dietary plant miRNAs derived from fresh fruits against the viral genome of the causative agent of COVID-19, specifically targeting the 3'UTR of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) genome. Expanding the analysis, we have also identified plant miRNAs that interact against the Omicron (B.1.1.529) variant of SARS-CoV-2 across 37 countries/territories throughout the world. This cross-species virus-plant interaction led us to identify the alignment of dietary plant miRNAs found in fruits like Citrus sinensis (Orange), Prunus persica (Peaches), Vitis vinifera (Grapes) and Malus domestica (Apple) onto the viral genomes. In particular, the interaction of C. sinensis miRNA - csi-miR169-3p and SARS-CoV-2 is noteworthy, as the targeted 3'UTR region "CTGCCT" is found conserved amongst all curated 772 Omicron variants across the globe. Hence this site "CTGCCT" and miRNA csi-miR169-3p may become promising therapeutic candidates to induce viral genome silencing. Thereby, this study reveals the mechanistic way of how fruits tend to enact a fight against viruses like SARS-CoV-2 and aid in maintaining a strong immune system of an individual.
MeSH term(s)	3' Untranslated Regions ; COVID-19/genetics ; Citrus sinensis/genetics ; Citrus sinensis/metabolism ; Fruit/genetics ; Malus ; MicroRNAs/metabolism ; SARS-CoV-2/genetics
Chemical Substances	3' Untranslated Regions ; MicroRNAs
Language	English
Publishing date	2022-04-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.105502
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