LIVIVO - Search results -

Search results

Result 1 - 10 of total 29

Search options

Article ; Online: Global conserved RBD fraction of SARS-CoV-2 S-protein with T500S mutation in silico significantly blocks ACE2 and rejects viral spike

Amrita Banerjee / Mehak Kanwar / Dipannita Santra / Smarajit Maiti

Translational Medicine Communications, Vol 7, Iss 1, Pp 1-

2022 Volume 11

Abstract: Abstract Background SARS-CoV-2 developed global-pandemic with millions of infections/deaths. As it is urgently necessary it is assumed that some blockers/inhibitors of ACE2 could be helpful to resist the binding of viral-spike Receptor-Binding-Domain ( ... ...

Abstract	Abstract Background SARS-CoV-2 developed global-pandemic with millions of infections/deaths. As it is urgently necessary it is assumed that some blockers/inhibitors of ACE2 could be helpful to resist the binding of viral-spike Receptor-Binding-Domain (RBD). Methods Here, conserved RBD from 186-countries were compared with WUHAN-Hu-1 wild-type (CLUSTAL-X2/Pymol). The RBD of ACE2-bound nCOV2 crystal-structure 6VW1 was analyzed by Haddock-PatchDock. Extensive structural study/trial to introduce point/double/triple mutations in the different locations of CUT4 (most-effective from total 4 proposed fragments; CUTs) were tested with Swiss-Model-Expacy. Results Blind-docking of mutated-CUTs in ACE2 completely rejected the nCOV2 binding to ACE2. Further, competitive-docking/binding-analyses (by PRODIGY) demonstrated few more bonding (LYS31-PHE490 and GLN42-GLN498) of CUT4 (than wild) and hindered TYR41-THR500 interaction with ACE2. Moreover, mutated-CUT4 even showed higher blocking effect against spike-ACE2 binding. Conclusion In summary, CUT4-mutant rejects whole glycosylated-nCoV2 in all pre-dock, post-dock and competitive-docking conditions. The present work strategy is relevant because it could be able to block at the first level entry of the virus to the host cells.
Keywords	SARS CoV-2 pandemic ; ACE2 blocking by RBD fragments ; Mutation in RBD ; T500S ; Haddock and Hawkdock ; Medicine ; R
Subject code	540
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Better binding informatics of delta variants (B.1.617.2) with ACE2 than wild, D614G or N501Y CoV-2 is fully blocked by 84 amino-acid cut of wild spike

Dipannita Santra / Amrita Banerjee / Smarajit Maiti

Informatics in Medicine Unlocked, Vol 29, Iss , Pp 100900- (2022)

2022

Abstract: Background and objective: The B.1.617.2 known as the Delta-variant harbors diverse Spike-mutations with developed transmissibility and immune-evasion more than wild/D614G/N501Y variants. The Delta-variant claimed comparatively a large number of lives ... ...

Abstract	Background and objective: The B.1.617.2 known as the Delta-variant harbors diverse Spike-mutations with developed transmissibility and immune-evasion more than wild/D614G/N501Y variants. The Delta-variant claimed comparatively a large number of lives globally. In the present study, the binding-affinities of these variants’ spikes to the human lung-ACE2 were investigated. Further, a certain portion of the spike-protein with a desired mutation was tested in-silico to block the ACE2. Methods: Structure of spike-variants were retrieved from PDB/GISAID and used for homology-modeling (SWISS-MODEL). A different combination of spike-ACE2 binding 1:1 or competitive blind-docking was performed using the Haddock 2.4 web-server. Eventually, two cut-segments (84 amino-acid of wild-spike, 432–516 Cut1) and its mutant T500S; Cut 2 were screened (Swiss-model Expasy-server) as blocker/inhibitor of all spike-variants (PyMOL-V2.2.2). Results: It is shown that the stability and energy of the Delta binding-affinity to ACE2 is far more than others. The number H-bonding (5), their lengths (1.7 Å-2.8 Å) and energy, Van-der-Walls energy, Haddock-score were highly favorable for more stable-binding of Delta-RBD to ACE2. The Ramachandran-plot (Zlab/UMassMed Bioinfo) data supports this. We observed the best Haddock score as −120.8±2.6 for Delta with Van-der-Walls and electrostatic-energy as −62.9 and −208.7, respectively. The highest binding-affinity (ΔG) was −10.7 kcal/mol. Its THR500 and GLN506 strongly bind with the LYS353 of ACE2. The Cut1 and its mutant T500S completely blocked Delta-spike binding to ACE2 with ΔG -8.4 and −10.6 kcal/mol, respectively. But during the comparison between 2 Cuts, Cut1 showed better results. Conclusions: Fractioned spike-protein from the conserved Receptor-Binding-Domain (RBD) could universally block the virus at entry-level, thus completely protecting any intercellular metabolism. Bioinformatics is an emerging field for screening of some drug/therapeutic targets from numerous options, minimizing time and expenses.
Keywords	SARS CoV-2 ; B.1.617.2- delta-variant ; Higher ACE2 affinity ; Spike-fragment peptide blocker ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	572
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Effects of theaflavin-gallate in-silico binding with different proteins of SARS-CoV-2 and host inflammation and vasoregulations referring an experimental rat-lung injury

Smarajit Maiti / Amrita Banerjee / Mehak Kanwar

Phytomedicine Plus, Vol 2, Iss 2, Pp 100237- (2022)

2022

Abstract: Background SARS-CoV-2 claimed 5,209,104 lives, infected 260,997,910 individuals, globally. Infection is caused due to exposure or susceptibility; deaths occur due to age,comorbidity,higher-viral-load, immuno-suppression, inflammation, and multi-organ ... ...

Abstract	Background SARS-CoV-2 claimed 5,209,104 lives, infected 260,997,910 individuals, globally. Infection is caused due to exposure or susceptibility; deaths occur due to age,comorbidity,higher-viral-load, immuno-suppression, inflammation, and multi-organ failure. Theaflavin-gallate, the major black tea component, showed previous evidence to inhibit HIV-1. Purpose As theaflavin-gallate prevents experimental rat-lung injury, the study of inhibitory effects of theaflavin-gallate was done, on SARS-CoV-2proteins and various host proteins related to some adverse effects in COVID-19 patients. Study Design Currently, some prospective phytochemical, black-tea (Camellia-sinensis) extract (BTE) was initially tested in vivo in strong oxidant-mutagen arsenic-induced model rat lung injury similar to that of COVID-19 manifestations like severe inflammation, oxidative stress, lung tissue degenerations, and apoptotic death. In silico, extensive bioinformatics and molecular docking experiments were performed on all catechin or theaflavin derivatives of C. sinensis, and finally theaflavin-3′-O-gallate (TFMG) were screened for blocking or inactivation of several proteins of SARS CoV-2 and host adversely-acting proteins or factors. Methods In vivo experiments in DNA stability (ladder, comet assay), free radicals attack (malondialdehyde; MDA, superoxide dismutase SOD, catalase gel-zymogram assay), extra cellular matrix damage (matrix metalloprotease; MMP2and9 zymogram assay) and inflammation (TNF-α, ELISA). In silico experiments- molecular docking by AutoDock-Patchdock analysis, Surface Topology Calculation by CASTp, Grid-value calculation, and Ramachandran Plot study. Results The BTE showed strong protection of lung DNA and cell-matrix by decreasing MMPs, TNF-α, and free radicals, the same factors affecting COVID-19 patients. In silico data suggest that TFMG significantly blocked the entry, exit, and amino acids at catalytic active-site of more than thirty proteins including viral (nsp1,nsp2,Mainpro,∼-9.0 kcal/mol) and host ...
Keywords	Global pandemic and SARS CoV-2 ; Inflammation and vaso-destabilizing proteins ; Theaflavin mono gallate ; Active site docking ; Therapeutic intervention ; Other systems of medicine ; RZ201-999
Subject code	500
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Airway management in pediatric facial burn contracture

Rishabh Agarwal / Mridul Dhar / Amrita Banerjee

Journal of Medical Sciences, Vol 41, Iss 4, Pp 211-

Safety, innovation, and expertise

2021 Volume 212

Keywords	Medicine ; R ; Medical emergencies. Critical care. Intensive care. First aid ; RC86-88.9
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Uptake and toxicity of polystyrene micro/nanoplastics in gastric cells

Amrita Banerjee / Lloyd O Billey / Weilin L Shelver

PLoS ONE, Vol 16, Iss 12, p e

Effects of particle size and surface functionalization.

2021 Volume 0260803

Abstract: Toxicity of micro or nanoplastics (MP/NP) in aquatic life is well-documented, however, information about the consequences of exposure to these particles in terrestrial species is scarce. This study was used to evaluate the uptake and/or toxicity of ... ...

Abstract	Toxicity of micro or nanoplastics (MP/NP) in aquatic life is well-documented, however, information about the consequences of exposure to these particles in terrestrial species is scarce. This study was used to evaluate the uptake and/or toxicity of polystyrene MP/NP in human gastric cells, comparing doses, particle sizes (50, 100, 200, 500, 1000 or 5000 nm) and surface functionalization (aminated, carboxylated or non-functionalized). In general, the uptake of 50 nm particles was significantly higher than 1000 nm particles. Among the 50 nm particles, the aminated particles were more avidly taken up by the cells and were cytotoxic at a lower concentration (≥ 7.5 μg/mL) compared to same sized carboxylated or non-functionalized particles (≥ 50 μg/mL). High toxicity of 50 nm aminated particles corresponded well with significantly high rates of apoptosis-necrosis induced by these particles in 4 h (29.2% of total cells) compared to all other particles (≤ 16.8%). The trend of apoptosis-necrosis induction by aminated particles in 4 h was 50 > 5000 > 1000 > 500 > 200 > 100 nm. The 50 nm carboxylated or non-functionalized particles also induced higher levels of apoptosis-necrosis in the cells compared to 100, 1000 and 5000 nm particles with same surface functionalization but longer exposure (24 h) to 50 nm carboxylated or non-functionalized particles significantly (p<0.0001) increased apoptosis-necrosis in the cells. The study demonstrated that the toxicity of MP/NP to gastric cells was dependent on particle size, dose surface functionalization and exposure period.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Uptake and toxicity of polystyrene micro/nanoplastics in gastric cells

Amrita Banerjee / Lloyd O. Billey / Weilin L. Shelver

PLoS ONE, Vol 16, Iss

Effects of particle size and surface functionalization

2021 Volume 12

Abstract	Toxicity of micro or nanoplastics (MP/NP) in aquatic life is well-documented, however, information about the consequences of exposure to these particles in terrestrial species is scarce. This study was used to evaluate the uptake and/or toxicity of polystyrene MP/NP in human gastric cells, comparing doses, particle sizes (50, 100, 200, 500, 1000 or 5000 nm) and surface functionalization (aminated, carboxylated or non-functionalized). In general, the uptake of 50 nm particles was significantly higher than 1000 nm particles. Among the 50 nm particles, the aminated particles were more avidly taken up by the cells and were cytotoxic at a lower concentration (≥ 7.5 μg/mL) compared to same sized carboxylated or non-functionalized particles (≥ 50 μg/mL). High toxicity of 50 nm aminated particles corresponded well with significantly high rates of apoptosis-necrosis induced by these particles in 4 h (29.2% of total cells) compared to all other particles (≤ 16.8%). The trend of apoptosis-necrosis induction by aminated particles in 4 h was 50 > 5000 > 1000 > 500 > 200 > 100 nm. The 50 nm carboxylated or non-functionalized particles also induced higher levels of apoptosis-necrosis in the cells compared to 100, 1000 and 5000 nm particles with same surface functionalization but longer exposure (24 h) to 50 nm carboxylated or non-functionalized particles significantly (p<0.0001) increased apoptosis-necrosis in the cells. The study demonstrated that the toxicity of MP/NP to gastric cells was dependent on particle size, dose surface functionalization and exposure period.
Keywords	Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Energetics and IC50 based epitope screening in SARS CoV-2 (COVID 19) spike protein by immunoinformatic analysis implicating for a suitable vaccine development

Amrita Banerjee / Dipannita Santra / Smarajit Maiti

Journal of Translational Medicine, Vol 18, Iss 1, Pp 1-

2020 Volume 14

Abstract: Abstract Background The recent outbreak by SARS-CoV-2 has generated a chaos in global health and economy and claimed/infected a large number of lives. Closely resembling with SARS CoV, the present strain has manifested exceptionally higher degree of ... ...

Abstract	Abstract Background The recent outbreak by SARS-CoV-2 has generated a chaos in global health and economy and claimed/infected a large number of lives. Closely resembling with SARS CoV, the present strain has manifested exceptionally higher degree of spreadability, virulence and stability possibly due to some unidentified mutations. The viral spike glycoprotein is very likely to interact with host Angiotensin-Converting Enzyme 2 (ACE2) and transmits its genetic materials and hijacks host machinery with extreme fidelity for self propagation. Few attempts have been made to develop a suitable vaccine or ACE2 blocker or virus-receptor inhibitor within this short period of time. Methods Here, attempt was taken to develop some therapeutic and vaccination strategies with a comparison of spike glycoproteins among SARS-CoV, MERS-CoV and the SARS-CoV-2. We verified their structure quality (SWISS-MODEL, Phyre2, and Pymol) topology (ProFunc), motifs (MEME Suite, GLAM2Scan), gene ontology based conserved domain (InterPro database) and screened several epitopes (SVMTrip) of SARS CoV-2 based on their energetics, IC50 and antigenicity with regard to their possible glycosylation and MHC/paratope binding (Vaxigen v2.0, HawkDock, ZDOCK Server) effects. Results We screened here few pairs of spike protein epitopic regions and selected their energetic, Inhibitory Concentration50 (IC50), MHC II reactivity and found some of those to be very good target for vaccination. A possible role of glycosylation on epitopic region showed profound effects on epitopic recognition. Conclusion The present work might be helpful for the urgent development of a suitable vaccination regimen against SARS CoV-2.
Keywords	SARS CoV-2 (COVID 19) ; Severe global outbreak-Dec 2019 ; Spike glycoprotein ; ACE-2 receptor protein ; Epitope designing and screening ; Vaccination ; Medicine ; R ; covid19
Subject code	570
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Controlled Delivery of Salmon Calcitonin Using Thermosensitive Triblock Copolymer Depot for Treatment of Osteoporosis

Lindsey Lipp / Divya Sharma / Amrita Banerjee / Jagdish Singh

ACS Omega, Vol 4, Iss 1, Pp 1157-

2019 Volume 1166

Keywords	Chemistry ; QD1-999
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	American Chemical Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Genetic diversity for drought and low-phosphorus tolerance in rice (Oryza sativa L.) varieties and donors adapted to rainfed drought-prone ecologies

Somnath Roy / B. C. Verma / Amrita Banerjee / J. Kumar / Uday Sankar Ray / N. P. Mandal

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 9

Abstract: Abstract Drought and phosphate availability are two major abiotic factors limiting productivity of rice in rainfed upland areas. There has been a constant need for new improved donor with tolerance to multiple abiotic stress conditions for rainfed rice ... ...

Abstract	Abstract Drought and phosphate availability are two major abiotic factors limiting productivity of rice in rainfed upland areas. There has been a constant need for new improved donor with tolerance to multiple abiotic stress conditions for rainfed rice breeding. In the present study, a set of 32 popular rice varieties and landraces were evaluated for drought and low-phosphorus (P) tolerance, and also characterized using grain yield under reproductive drought QTLs (DTY QTLs) and Pup1 linked/specific molecular markers. Twenty-seven genotypes were identified as tolerant to moderately tolerant to drought. The SSR markers linked to ten DTY QTLs classified the genotypes into two groups corresponding to aus and indica. The tolerant genotypes were distributed under both groups. Based on the core markers of Pup1 locus, complete tolerant haplotype was recorded in nine genotypes other than the tolerant check Dular. Nine more genotypes showed the incomplete tolerant haplotypes. The rice genotypes showed significantly high genetic variability for low-P tolerance in hydroponic study. A few genotypes revealed non-Pup1 type tolerance which needs further confirmation.
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Molecular co-localization of multiple drugs in a nanoscopic delivery vehicle for potential synergistic remediation of multi-drug resistant bacteria

Amrita Banerjee / Dipanjan Mukherjee / Arpan Bera / Ria Ghosh / Susmita Mondal / Subhadipta Mukhopadhyay / Ranjan Das / Hatem M. Altass / Sameer. S. A. Natto / Ziad Moussa / Saleh A. Ahmed / Arpita Chattopadhyay / Samir Kumar Pal

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 17

Abstract: Abstract Anti-microbial resistant infection is predicted to be alarming in upcoming years. In the present study, we proposed co-localization of two model drugs viz., rifampicin and benzothiazole used in anti-tuberculosis and anti-fungal agents ... ...

Abstract	Abstract Anti-microbial resistant infection is predicted to be alarming in upcoming years. In the present study, we proposed co-localization of two model drugs viz., rifampicin and benzothiazole used in anti-tuberculosis and anti-fungal agents respectively in a nanoscopic cationic micelle (cetyl triethyl ammonium bromide) with hydrodynamic diameter of 2.69 nm. Sterilization effect of the co-localized micellar formulation against a model multi-drug resistant bacterial strain viz., Methicillin resistant Staphylococcus aureus was also investigated. 99.88% decrease of bacterial growth in terms of colony forming unit was observed using the developed formulation. While Dynamic Light Scattering and Forsters Resonance Energy Transfer between benzothiazole and rifampicin show co-localization of the drugs in the nanoscopic micellar environment, analysis of time-resolved fluorescence decays by Infelta-Tachiya model and the probability distribution of the donor–acceptor distance fluctuations for 5 μM,10 μM and 15 μM acceptor concentrations confirm efficacy of the co-localization. Energy transfer efficiency and the donor acceptor distance are found to be 46% and 20.9 Å respectively. We have also used a detailed computational biology framework to rationalize the sterilization effect of our indigenous formulation. It has to be noted that the drugs used in our studies are not being used for their conventional indication. Rather the co-localization of the drugs in the micellar environment shows a completely different indication of their use in the remediation of multi-drug resistant bacteria revealing the re-purposing of the drugs for potential use in hospital-born multi-drug resistant bacterial infection.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2022-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED