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Article: Natural selection of the D614G mutation in SARS-CoV-2 Omicron (B.1.1.529) variant and its subvariants.

Chakraborty, Chiranjib / Saha, Abinit / Bhattacharya, Manojit / Dhama, Kuldeep / Agoramoorthy, Govindasamy

2023 Volume 31, Page(s) 437–439

Language	English
Publishing date	2023-02-13
Publishing country	United States
Document type	News
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2023.01.013
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genome structure and genetic diversity in the Ebola virus.

Ghosh, Sanmitra / Saha, Abinit / Samanta, Saikat / Saha, Rudra P

Current opinion in pharmacology

2021 Volume 60, Page(s) 83–90

Abstract: Ebola is a deadly pathogen responsible for Ebola virus disease, first came to prominence in the year 1976. This rapidly evolving virus imposed a serious threat to the human population in the last few decades and also continues to be a probable threat to ... ...

Abstract	Ebola is a deadly pathogen responsible for Ebola virus disease, first came to prominence in the year 1976. This rapidly evolving virus imposed a serious threat to the human population in the last few decades and also continues to be a probable threat to our race. A better understanding of the virus in terms of its genomic structure is very much needed to develop an effective antiviral therapy against this deadly pathogen. Complete knowledge of its genomic structure and variations will help us and the entire scientific community to design effective therapy in terms of either vaccine development or the development of proper antiviral medicine.
MeSH term(s)	Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Ebolavirus/genetics ; Genetic Variation ; Genomics ; Hemorrhagic Fever, Ebola/drug therapy ; Humans
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2021-08-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2037057-X
ISSN	1471-4973 ; 1471-4892
ISSN (online)	1471-4973
ISSN	1471-4892
DOI	10.1016/j.coph.2021.06.010
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Article ; Online: Recent progress of circular RNAs in different types of human cancer: Technological landscape, clinical opportunities and challenges (Review).

Sharma, Ashish Ranjan / Banerjee, Shreya / Bhattacharya, Manojit / Saha, Abinit / Lee, Sang-Soo / Chakraborty, Chiranjib

International journal of oncology

2022 Volume 60, Issue 5

Abstract: Circular RNAs (circRNAs) are a novel class of endogenous non‑coding RNAs that have been recently regarded as functionally active. CircRNAs are remarkably stable and known to possess several biological functions such as microRNA sponging, regulating ... ...

Abstract	Circular RNAs (circRNAs) are a novel class of endogenous non‑coding RNAs that have been recently regarded as functionally active. CircRNAs are remarkably stable and known to possess several biological functions such as microRNA sponging, regulating transcription and splicing and occasionally acting as polypeptide‑producing templates. CircRNAs show tissue‑specific expression and have been reported to be associated with the progression of several types of malignancies. Given the recent progress in genome sequencing and bioinformatics techniques, a rapid increment in the biological role of circRNAs has been observed. Concurrently, the patent search from different patent databases shows that the patent number of circRNA is increasing very quickly. These phenomena reveal a rapid development of the technological landscape. In the present review, the recent progress on circRNAs in various kinds of cancer has been investigated and their function as biomarkers or therapeutic targets and their technological landscape have been appreciated. A new insight into circRNAs structure and functional capabilities in cancer has been reviewed. Continually increasing knowledge on their critical role during cancer progression is projecting them as biomarkers or therapeutic targets for various kinds of cancer. Thus, recent updates on the functional role of circRNAs in terms of the technological landscape, clinical opportunities (biomarkers and therapeutic targets), and challenges in cancer have been illustrated.
MeSH term(s)	Biomarkers/metabolism ; Humans ; MicroRNAs/genetics ; Neoplasms/pathology ; RNA Splicing ; RNA, Circular/genetics
Chemical Substances	Biomarkers ; MicroRNAs ; RNA, Circular
Language	English
Publishing date	2022-04-01
Publishing country	Greece
Document type	Journal Article ; Review
ZDB-ID	1154403-x
ISSN	1791-2423 ; 1019-6439
ISSN (online)	1791-2423
ISSN	1019-6439
DOI	10.3892/ijo.2022.5346
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Article ; Online: Effect of ZnO quantum dots on Escherichia coli global transcription regulator: A molecular investigation.

Saha, Abinit / Chakraborti, Soumyananda

International journal of biological macromolecules

2018 Volume 117, Page(s) 1280–1288

Abstract: ZnO quantum dots (QDs) are very well known for their antimicrobial activity against several bacteria, however, we still do not know any protein targets of ZnO QDs. In order to determine possible protein target, interaction of ZnO QDs was studied with CRP ...

Abstract	ZnO quantum dots (QDs) are very well known for their antimicrobial activity against several bacteria, however, we still do not know any protein targets of ZnO QDs. In order to determine possible protein target, interaction of ZnO QDs was studied with CRP (Cyclic AMP Receptor Protein), a global transcription regulator protein. Binding between ZnO QDs and E. coli CRP was mainly studied by isothermal titration calorimetry (ITC), structural changes of protein were monitored by fluorescence and circular dichroism spectroscopy, and in-vitro transcription assay was used to asses CRP activity. Result shows that both electrostatic and hydrophobic interactions are involved in CRP-ZnO binding. Different spectroscopic investigation revealed that ZnO binding to CRP leads to extensive unfolding and destabilization, which ultimately leads to protein aggregation. It was also observed that in presence of ZnO dimerization ability of CRP was sharply reduced. In-vitro transcription assay also shows that CRP activity gets severely compromised on ZnO binding. All our data suggests that ZnO QD binding to CRP and consequent structural and functional changes most probably plays a crucial role in ZnO QD induced antimicrobial action.
MeSH term(s)	Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Binding Sites ; Circular Dichroism ; Cyclic AMP Receptor Protein/chemistry ; Escherichia coli/drug effects ; Escherichia coli/genetics ; Gene Expression Regulation, Bacterial/drug effects ; Protein Binding ; Protein Conformation ; Protein Stability ; Protein Unfolding ; Quantum Dots/chemistry ; Structure-Activity Relationship ; Thermodynamics ; Transcriptional Activation ; Transcriptome ; Zinc Oxide/chemistry
Chemical Substances	Anti-Bacterial Agents ; Cyclic AMP Receptor Protein ; Zinc Oxide (SOI2LOH54Z)
Language	English
Publishing date	2018-06-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2018.06.001
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Article ; Online: Revealing the structural and molecular interaction landscape of the favipiravir-RTP and SARS-CoV-2 RdRp complex through integrative bioinformatics

Chiranjib Chakraborty / Manojit Bhattacharya / Abinit Saha / Abdulrahman Alshammari / Metab Alharbi / G. Saikumar / Soumen Pal / Kuldeep Dhama / Sang-Soo Lee

Journal of Infection and Public Health, Vol 16, Iss 7, Pp 1048-

Insights for developing potent drugs targeting SARS-CoV-2 and other viruses

2023 Volume 1056

Abstract: Background: The global research community has made considerable progress in therapeutic and vaccine research during the COVID-19 pandemic. Several therapeutics have been repurposed for the treatment of COVID-19. One such compound is, favipiravir, which ... ...

Abstract	Background: The global research community has made considerable progress in therapeutic and vaccine research during the COVID-19 pandemic. Several therapeutics have been repurposed for the treatment of COVID-19. One such compound is, favipiravir, which was approved for the treatment of influenza viruses, including drug-resistant influenza. Despite the limited information on its molecular activity, clinical trials have attempted to determine the effectiveness of favipiravir in patients with mild to moderate COVID-19. Here, we report the structural and molecular interaction landscape of the macromolecular complex of favipiravir-RTP and SARS-CoV-2 RdRp with the RNA chain. Methods: Integrative bioinformatics was used to reveal the structural and molecular interaction landscapes of two macromolecular complexes retrieved from RCSB PDB. Results: We analyzed the interactive residues, H-bonds, and interaction interfaces to evaluate the structural and molecular interaction landscapes of the two macromolecular complexes. We found seven and six H-bonds in the first and second interaction landscapes, respectively. The maximum bond length is 3.79 Å. In the hydrophobic interactions, five residues (Asp618, Asp760, Thr687, Asp623, and Val557) were associated with the first complex and two residues (Lys73 and Tyr217) were associated with the second complex. The mobilities, collective motion, and B-factor of the two macromolecular complexes were analyzed. Finally, we developed different models, including trees, clusters, and heat maps of antiviral molecules, to evaluate the therapeutic status of favipiravir as an antiviral drug. Conclusions: The results revealed the structural and molecular interaction landscape of the binding mode of favipiravir with the nsp7–nsp8–nsp12-RNA SARS-CoV-2 RdRp complex. Our findings can help future researchers in understanding the mechanism underlying viral action and guide the design of nucleotide analogs that mimic favipiravir and exhibit greater potency as antiviral drugs against SARS-CoV-2 and ...
Keywords	Favipiravir-RTP ; RdRp complex ; Structural and molecular interaction ; SARS-CoV-2 ; Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
Subject code	540
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Revealing the structural and molecular interaction landscape of the favipiravir-RTP and SARS-CoV-2 RdRp complex through integrative bioinformatics: Insights for developing potent drugs targeting SARS-CoV-2 and other viruses.

Chakraborty, Chiranjib / Bhattacharya, Manojit / Saha, Abinit / Alshammari, Abdulrahman / Alharbi, Metab / Saikumar, G / Pal, Soumen / Dhama, Kuldeep / Lee, Sang-Soo

Journal of infection and public health

2023 Volume 16, Issue 7, Page(s) 1048–1056

Abstract	Background: The global research community has made considerable progress in therapeutic and vaccine research during the COVID-19 pandemic. Several therapeutics have been repurposed for the treatment of COVID-19. One such compound is, favipiravir, which was approved for the treatment of influenza viruses, including drug-resistant influenza. Despite the limited information on its molecular activity, clinical trials have attempted to determine the effectiveness of favipiravir in patients with mild to moderate COVID-19. Here, we report the structural and molecular interaction landscape of the macromolecular complex of favipiravir-RTP and SARS-CoV-2 RdRp with the RNA chain. Methods: Integrative bioinformatics was used to reveal the structural and molecular interaction landscapes of two macromolecular complexes retrieved from RCSB PDB. Results: We analyzed the interactive residues, H-bonds, and interaction interfaces to evaluate the structural and molecular interaction landscapes of the two macromolecular complexes. We found seven and six H-bonds in the first and second interaction landscapes, respectively. The maximum bond length is 3.79 Å. In the hydrophobic interactions, five residues (Asp618, Asp760, Thr687, Asp623, and Val557) were associated with the first complex and two residues (Lys73 and Tyr217) were associated with the second complex. The mobilities, collective motion, and B-factor of the two macromolecular complexes were analyzed. Finally, we developed different models, including trees, clusters, and heat maps of antiviral molecules, to evaluate the therapeutic status of favipiravir as an antiviral drug. Conclusions: The results revealed the structural and molecular interaction landscape of the binding mode of favipiravir with the nsp7-nsp8-nsp12-RNA SARS-CoV-2 RdRp complex. Our findings can help future researchers in understanding the mechanism underlying viral action and guide the design of nucleotide analogs that mimic favipiravir and exhibit greater potency as antiviral drugs against SARS-CoV-2 and other infectious viruses. Thus, our work can help in preparing for future epidemics and pandemics.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19 ; Pandemics ; RNA-Dependent RNA Polymerase ; RNA ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Antiviral Agents/chemistry
Chemical Substances	favipiravir (EW5GL2X7E0) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; RNA (63231-63-0) ; Antiviral Agents
Language	English
Publishing date	2023-05-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2467587-8
ISSN	1876-035X ; 1876-0341
ISSN (online)	1876-035X
ISSN	1876-0341
DOI	10.1016/j.jiph.2023.05.010
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: D614G mutation eventuates in all VOI and VOC in SARS-CoV-2: Is it part of the positive selection pioneered by Darwin?

Chakraborty, Chiranjib / Saha, Abinit / Sharma, Ashish Ranjan / Bhattacharya, Manojit / Lee, Sang-Soo / Agoramoorthy, Govindasamy

Molecular therapy. Nucleic acids

2021 Volume 26, Page(s) 237–241

Abstract: Recently, several emerging variants of SARS-CoV-2 have originated from the Wuhan strain and spread throughout the globe within one and a half years. One mutation, D614G, is very prominent in all VOI and VOC in SARS-CoV-2. This mutation might help to ... ...

Abstract	Recently, several emerging variants of SARS-CoV-2 have originated from the Wuhan strain and spread throughout the globe within one and a half years. One mutation, D614G, is very prominent in all VOI and VOC in SARS-CoV-2. This mutation might help to increase the viral fitness in all emerging variants where the mutation is present. With the help of this mutation (D614G), the SARS-CoV-2 variants have gained viral fitness to enhance viral replication and increase transmission. This paper attempts to answer the question of whether the mutation (D614G) occurs due to positive selection or not.
Language	English
Publishing date	2021-09-01
Publishing country	United States
Document type	Editorial
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2021.07.011
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Article ; Online: Prokaryotic ncRNAs

Rajib Majumder / Sanmitra Ghosh / Arpita Das / Manoj Kumar Singh / Saikat Samanta / Abinit Saha / Rudra P. Saha

Current Research in Pharmacology and Drug Discovery, Vol 3, Iss , Pp 100136- (2022)

Master regulators of gene expression

2022

Abstract: ncRNA plays a very pivotal role in various biological activities ranging from gene regulation to controlling important developmental networks. It is imperative to note that this small molecule is not only present in all three domains of cellular life, ... ...

Abstract	ncRNA plays a very pivotal role in various biological activities ranging from gene regulation to controlling important developmental networks. It is imperative to note that this small molecule is not only present in all three domains of cellular life, but is an important modulator of gene regulation too in all these domains. In this review, we discussed various aspects of ncRNA biology, especially their role in bacteria. The last two decades of scientific research have proved that this molecule plays an important role in the modulation of various regulatory pathways in bacteria including the adaptive immune system and gene regulation. It is also very surprising to note that this small molecule is also employed in various processes related to the pathogenicity of virulent microorganisms.
Keywords	ncRNA ; Prokaryotic ncRNA ; Bacterial ncRNA ; ncRNA biology ; Gene regulation ; CRISPR ; Therapeutics. Pharmacology ; RM1-950
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Effect of ZnO quantum dots on Escherichia coli global transcription regulator: A molecular investigation

Saha, Abinit / Soumyananda Chakraborti

International journal of biological macromolecules. 2018 Oct. 01, v. 117

2018

Abstract	ZnO quantum dots (QDs) are very well known for their antimicrobial activity against several bacteria, however, we still do not know any protein targets of ZnO QDs. In order to determine possible protein target, interaction of ZnO QDs was studied with CRP (Cyclic AMP Receptor Protein), a global transcription regulator protein. Binding between ZnO QDs and E. coli CRP was mainly studied by isothermal titration calorimetry (ITC), structural changes of protein were monitored by fluorescence and circular dichroism spectroscopy, and in-vitro transcription assay was used to asses CRP activity. Result shows that both electrostatic and hydrophobic interactions are involved in CRP-ZnO binding. Different spectroscopic investigation revealed that ZnO binding to CRP leads to extensive unfolding and destabilization, which ultimately leads to protein aggregation. It was also observed that in presence of ZnO dimerization ability of CRP was sharply reduced. In-vitro transcription assay also shows that CRP activity gets severely compromised on ZnO binding. All our data suggests that ZnO QD binding to CRP and consequent structural and functional changes most probably plays a crucial role in ZnO QD induced antimicrobial action.
Keywords	antimicrobial properties ; bacteria ; calorimetry ; circular dichroism spectroscopy ; cyclic AMP ; dimerization ; Escherichia coli ; fluorescence ; hydrophobic bonding ; quantum dots ; regulatory proteins ; spectral analysis ; titration ; transcription factors ; zinc oxide
Language	English
Dates of publication	2018-1001
Size	p. 1280-1288.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2018.06.001
Database	NAL-Catalogue (AGRICOLA)

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Article: Recent research progress on circular RNAs: Biogenesis, properties, functions, and therapeutic potential.

Sharma, Ashish Ranjan / Bhattacharya, Manojit / Bhakta, Swarnav / Saha, Abinit / Lee, Sang-Soo / Chakraborty, Chiranjib

Molecular therapy. Nucleic acids

2021 Volume 25, Page(s) 355–371

Abstract: Circular RNAs (circRNAs), an emerging family member of RNAs, have gained importance in research due to their new functional roles in cellular physiology and disease progression. circRNAs are usually available in a wide range of cells and have shown ... ...

Abstract	Circular RNAs (circRNAs), an emerging family member of RNAs, have gained importance in research due to their new functional roles in cellular physiology and disease progression. circRNAs are usually available in a wide range of cells and have shown tissue-specific expression as well as developmental specific expression. circRNAs are characterized by structural stability, conservation, and high abundance in the cell. In this review, we discuss the different models of biogenesis. The properties of circRNAs such as localization, structure and conserved pattern, stability, and expression specificity are also been illustrated. Furthermore, we discuss the biological functions of circRNAs such as microRNA (miRNA) sponging, cell cycle regulation, cell-to-cell communication, transcription regulation, translational regulation, disease diagnosis, and therapeutic potential. Finally, we discuss the recent research progress and future perspective of circRNAs. This review provides an understanding of potential diagnostic markers and the therapeutic potential of circRNAs, which are emerging daily.
Language	English
Publishing date	2021-06-04
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2021.05.022
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