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Article ; Online: In silico

Mitra, Debarghya / Pandey, Janmejay / Jain, Alok / Swaroop, Shiv

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 11, Page(s) 5189–5202

Abstract: SARS-CoV-2 has been efficient in ensuring that many countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia, and economic recession, the virus has brought together countries to look at possible therapeutic ...

Abstract	SARS-CoV-2 has been efficient in ensuring that many countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia, and economic recession, the virus has brought together countries to look at possible therapeutic countermeasures. With prophylactic interventions possibly months away from being particularly effective, a slew of measures and possibilities concerning the design of vaccines are being worked upon. We attempted a structure-based approach utilizing a combination of epitope prediction servers and Molecular dynamic (MD) simulations to develop a multi-epitope-based subunit vaccine that involves the two subunits of the spike glycoprotein of SARS-CoV-2 (S1 and S2) coupled with a substantially effective chimeric adjuvant to create stable vaccine constructs. The designed constructs were evaluated based on their docking with Toll-Like Receptor (TLR) 4. Our findings provide an epitope-based peptide fragment that can be a potential candidate for the development of a vaccine against SARS-CoV-2. Recent experimental studies based on determining immunodominant regions across the spike glycoprotein of SARS-CoV-2 indicate the presence of the predicted epitopes included in this study.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	COVID-19/prevention & control ; COVID-19 Vaccines/immunology ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Humans ; Molecular Docking Simulation ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/immunology ; Vaccines, Subunit/immunology
Chemical Substances	COVID-19 Vaccines ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Spike Glycoprotein, Coronavirus ; Vaccines, Subunit ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-01-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1869092
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Combining cysteine scanning with chemical labeling to map protein-protein interactions and infer bound structure in an intrinsically disordered region.

Ahmed, Shahbaz / Chattopadhyay, Gopinath / Manjunath, Kavyashree / Bhasin, Munmun / Singh, Neelam / Rasool, Mubashir / Das, Sayan / Rana, Varsha / Khan, Neha / Mitra, Debarghya / Asok, Aparna / Singh, Ramandeep / Varadarajan, Raghavan

Frontiers in molecular biosciences

2022 Volume 9, Page(s) 997653

Abstract: ... ...

Abstract	The
Language	English
Publishing date	2022-10-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.997653
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mapping of Methyl Epitopes of a Peptide-Drug with Its Receptor by 2D STDD-Methyl TROSY NMR Spectroscopy.

Dey, Anomitra / Mitra, Debarghya / Rachineni, Kavitha / Khatri, Lakshya Raj / Paithankar, Harshad / Vajpai, Navratna / Kumar, Ashutosh

Chembiochem : a European journal of chemical biology

2022 Volume 23, Issue 23, Page(s) e202200489

Abstract: The current trend in the biopharmaceutical market has boosted the development and production of biological drugs with high efficacy and fidelity for receptor binding. While high-resolution structural insights into binding epitopes of the receptor are ... ...

Abstract	The current trend in the biopharmaceutical market has boosted the development and production of biological drugs with high efficacy and fidelity for receptor binding. While high-resolution structural insights into binding epitopes of the receptor are indispensable for better therapeutic design, it is tedious and costly. In this work, we develop a protocol by integrating two well-known NMR-based solution-state methods. Saturation transfer double-difference with methyl-TROSY (STDD-Methyl TROSY NMR) was used to probe methyl binding epitopes of the ligand in a label-free environment. This study was carried out with Human insulin as a model peptide drug, with the insulin growth factor receptor (IGFR), which is an off-target receptor for insulin. Methyl epitopes identified from STDD-Methyl TROSY NMR spectroscopy were validated through the HADDOCK platform to generate a drug-receptor model. Since this method can be applied at natural abundance, it has the potential to screen a large set of peptide-drug interactions for optimum receptor binding. Thus, we propose STDD-Methyl TROSY NMR spectroscopy as a technique for rapid screening of biologics for the development of optimized biopharmaceutics.
MeSH term(s)	Humans ; Epitopes ; Magnetic Resonance Spectroscopy/methods ; Ligands ; Peptides ; Insulins ; Nuclear Magnetic Resonance, Biomolecular/methods
Chemical Substances	Epitopes ; Ligands ; Peptides ; Insulins
Language	English
Publishing date	2022-11-10
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020469-3
ISSN	1439-7633 ; 1439-4227
ISSN (online)	1439-7633
ISSN	1439-4227
DOI	10.1002/cbic.202200489
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Free spermidine evokes superoxide radicals that manifest toxicity.

Kumar, Vineet / Mishra, Rajesh Kumar / Ghose, Debarghya / Kalita, Arunima / Dhiman, Pulkit / Prakash, Anand / Thakur, Nirja / Mitra, Gopa / Chaudhari, Vinod D / Arora, Amit / Dutta, Dipak

eLife

2022 Volume 11

Abstract: Spermidine and other polyamines alleviate oxidative stress, yet excess spermidine seems toxic ... ...

Abstract	Spermidine and other polyamines alleviate oxidative stress, yet excess spermidine seems toxic to
MeSH term(s)	Escherichia coli/genetics ; Iron/toxicity ; Reactive Oxygen Species ; Spermidine ; Superoxides
Chemical Substances	Reactive Oxygen Species ; Superoxides (11062-77-4) ; Iron (E1UOL152H7) ; Spermidine (U87FK77H25)
Language	English
Publishing date	2022-04-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.77704
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Article ; Online: Evaluation of (Anti)androgenic Activities of Environmental Xenobiotics in Milk Using a Human Liver Cell Line and Androgen Receptor-Based Promoter-Reporter Assay.

Agrawal, Himanshu / Thakur, Keshav / Mitra, Shreyasi / Mitra, Debarghya / Keswani, Chetan / Sircar, Debabrata / Onteru, Suneel / Singh, Dheer / Singh, Surya P / Tyagi, Rakesh K / Roy, Partha

ACS omega

2022 Volume 7, Issue 45, Page(s) 41531–41547

Abstract: The recent reports on milk consumption and its associated risk with hormone related disorders necessitates the evaluation of dairy products for the presence of endocrine disrupting chemicals (EDCs) and ensure the safety of consumers. In view of this, we ... ...

Abstract	The recent reports on milk consumption and its associated risk with hormone related disorders necessitates the evaluation of dairy products for the presence of endocrine disrupting chemicals (EDCs) and ensure the safety of consumers. In view of this, we investigated the possible presence of (anti)androgenic contaminants in raw and commercialized milk samples. For this purpose, a novel HepARE-Luc cell line that stably expresses human androgen receptor (AR) and the androgen responsive luciferase reporter gene was generated and used in the present study. Treatment of this cell line with androgens and corresponding antiandrogen (flutamide) stimulated or inhibited expression of reporter luciferase, respectively. Real time polymerase chain reaction and immunostaining results exhibited transcription response and translocation of AR from the cytoplasm to the nucleus in response to androgen. Observations implied that a cell-based xenobiotic screening assay
Language	English
Publishing date	2022-11-04
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.2c05344
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Article ; Online: Multi-epitope-based peptide vaccine design against SARS-CoV-2 using its spike protein

Mitra, Debarghya / Pandey, Janmejay / Swaroop, Shiv

bioRxiv

Abstract: SARS CoV-2 has particularly been efficient in ensuring that many countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia and economic recession, the virus has brought together countries in order to look at ...

Abstract	SARS CoV-2 has particularly been efficient in ensuring that many countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia and economic recession, the virus has brought together countries in order to look at possible therapeutic countermeasures. With prophylactic interventions possibly months away from being particularly effective, a slew of measures and possibilities concerning the design of vaccines are being worked upon. We attempted a structure-based approach utilizing a combination of epitope prediction servers to develop a multi-epitope-based subunit vaccine that involves the two major domains of the spike glycoprotein of SARS CoV-2 (S1 and S2) coupled with a substantially effective chimeric adjuvant to create stable vaccine constructs through MD simulations. The designed constructs were evaluated based on their docking with Toll Like Receptor (TLR) 4. Our findings provide an epitope-based peptide fragment; which can be a potential candidate for the development of a vaccine against SARS-CoV-2. Recent experimental studies based on determining immunodominant regions across the spike glycoprotein of SARS-CoV-2 indicate the presence of the predicted epitopes included in this study.
Keywords	covid19
Publisher	BioRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.04.23.055467
Database	COVID19

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Article ; Online: Investigation of the interaction of allergens of Glycine max with IgE-antibody for designing of peptidomimetics based anti-allergen.

Tiwari, Vishvanath / Mitra, Debarghya / Tiwari, Monalisa

International immunopharmacology

2018 Volume 61, Page(s) 394–404

Abstract: Allergen induced IgE dependent type I hypersensitivity is the main cause of the allergy, which would be a burden on medical setup in coming years. Allergens of Glycine max have been isolated, and their disease relationships are documented. Therefore, it ... ...

Abstract	Allergen induced IgE dependent type I hypersensitivity is the main cause of the allergy, which would be a burden on medical setup in coming years. Allergens of Glycine max have been isolated, and their disease relationships are documented. Therefore, it becomes important to investigate the interaction of different allergens of Glycine max with IgE and also screen suitable therapeutics to prevent this interaction. The amino acid sequences of all allergens of Glycine max and their isoallergens have been taken, and 3D structure of allergens (Gly m 3, Gly m 4, Gly m 5, Gly m 6 and Gly m 8) and their isoallergens were generated using Modeller v9.17. The modeled structures were further validated using PSVS, ProSA, RAMPAGE, and PDBsum. HL domain of Fab region of human IgE (PDBID: 2R56) was generated using UCSFchimera. The HL domain was minimized by Schrodinger software using the OPLS_2005 force field. SiteMap identified epitope binding site of the minimized domain. All the predicted epitopes of different allergens were docked to the binding site of HL domain using the Patchdock server. We have also designed a peptidomimetics based inhibitor targeted at interaction interface of Gly m8 and IgE, using in-silico virtual screening, molecular mechanics, and molecular dynamics simulation studies. These studies identified BDE32166344 ((N-(1-{[1-(1-aminocyclopentanecarbonyl)-3-hydroxypyrrolidin-3-yl]methyl}piperidin-4-yl)acetamide) as a peptidomimetics based lead with binding energy of -72.77 kcal/mol. Therefore, the present study investigates the interaction between different Gly m allergens and IgE antibody and identifies peptidomimetics based lead that might be developed as a suitable therapeutics against allergy caused by allergen of Glycine max.
MeSH term(s)	Allergens/immunology ; Allergens/metabolism ; Antigens, Plant/immunology ; Antigens, Plant/metabolism ; Computer Simulation ; Cross Reactions ; Drug Design ; Epitopes/metabolism ; Fabaceae/immunology ; Humans ; Hypersensitivity, Immediate/immunology ; Hypersensitivity, Immediate/therapy ; Immunoglobulin E/metabolism ; Models, Molecular ; Peptidomimetics ; Protein Binding ; Protein Structure, Tertiary ; Glycine max/immunology ; Glycine max/metabolism
Chemical Substances	Allergens ; Antigens, Plant ; Epitopes ; Peptidomimetics ; Immunoglobulin E (37341-29-0)
Language	English
Publishing date	2018-06-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2043785-7
ISSN	1878-1705 ; 1567-5769
ISSN (online)	1878-1705
ISSN	1567-5769
DOI	10.1016/j.intimp.2018.06.023
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Article ; Online: Multi-epitope based peptide vaccine design against SARS-CoV-2 using its spike protein

Mitra, Debarghya / Shekhar, Nishant / Pandey, Janmejay / Jain, Alok / Swaroop, Shiv

bioRxiv

Abstract: SARS CoV-2 has particularly been efficient in ensuring that entire countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia and economic recession the virus has brought together countries in order to look ... ...

Abstract	SARS CoV-2 has particularly been efficient in ensuring that entire countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia and economic recession the virus has brought together countries in order to look at possible therapeutic countermeasures. With prophylactic interventions possibly months away from particularly being effective, a slew of measures and possibilities concerning design of vaccines are being worked upon. We attempt a structure based approach utilizing a combination of epitope prediction servers to develop a multi-epitope based subunit vaccine that involves the two major domains of the spike glycoprotein of SARS CoV-2 ( S1 and S2) coupled with a substantially effective chimeric adjuvant acting as a triagonist to substantially create stable vaccine constructs through MD simulations. The designed constructs are evaluated based on their docking with Toll Like Receptor (TLR) 4. Our findings provide epitope-based peptide fragment which can be potential candidates for development of vaccine against SARS-CoV-2.
Keywords	covid19
Language	English
Publishing date	2020-04-24
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2020.04.23.055467
Database	COVID19

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Article ; Online: Multi-epitope based peptide vaccine design against SARS-CoV-2 using its spike protein

Mitra, Debarghya / Shekhar, Nishant / Pandey, Janmejay / Jain, Alok / Swaroop, Shiv

bioRxiv

Abstract	SARS CoV-2 has particularly been efficient in ensuring that entire countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia and economic recession the virus has brought together countries in order to look at possible therapeutic countermeasures. With prophylactic interventions possibly months away from particularly being effective, a slew of measures and possibilities concerning design of vaccines are being worked upon. We attempt a structure based approach utilizing a combination of epitope prediction servers to develop a multi-epitope based subunit vaccine that involves the two major domains of the spike glycoprotein of SARS CoV-2 (S1 and S2) coupled with a substantially effective chimeric adjuvant to create stable vaccine constructs through MD simulations. The designed constructs are evaluated based on their docking with Toll Like Receptor (TLR) 4. Our findings provide epitope-based peptide fragment which can be potential candidate for development of vaccine against SARS-CoV-2. Recent experimental studies based on determining immunodominant regions across the spike glycoprotein of SARS-CoV-2 indicate the presence of the predicted epitopes included in this study.
Keywords	covid19
Publisher	BioRxiv
Document type	Article ; Online
DOI	10.1101/2020.04.23.055467
Database	COVID19

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Article ; Online: Free spermidine evokes superoxide radicals that manifest toxicity

Vineet Kumar / Rajesh Kumar Mishra / Debarghya Ghose / Arunima Kalita / Pulkit Dhiman / Anand Prakash / Nirja Thakur / Gopa Mitra / Vinod D Chaudhari / Amit Arora / Dipak Dutta

eLife, Vol

2022 Volume 11

Abstract: Spermidine and other polyamines alleviate oxidative stress, yet excess spermidine seems toxic to Escherichia coli unless it is neutralized by SpeG, an enzyme for the spermidine N-acetyl transferase function. Thus, wild-type E. coli can tolerate applied ... ...

Abstract	Spermidine and other polyamines alleviate oxidative stress, yet excess spermidine seems toxic to Escherichia coli unless it is neutralized by SpeG, an enzyme for the spermidine N-acetyl transferase function. Thus, wild-type E. coli can tolerate applied exogenous spermidine stress, but ΔspeG strain of E. coli fails to do that. Here, using different reactive oxygen species (ROS) probes and performing electron paramagnetic resonance spectroscopy, we provide evidence that although spermidine mitigates oxidative stress by lowering overall ROS levels, excess of it simultaneously triggers the production of superoxide radicals, thereby causing toxicity in the ΔspeG strain. Furthermore, performing microarray experiment and other biochemical assays, we show that the spermidine-induced superoxide anions affected redox balance and iron homeostasis. Finally, we demonstrate that while RNA-bound spermidine inhibits iron oxidation, free spermidine interacts and oxidizes the iron to evoke superoxide radicals directly. Therefore, we propose that the spermidine-induced superoxide generation is one of the major causes of spermidine toxicity in E. coli.
Keywords	Escherichia coli ; SpeG ; spermidine toxicity ; superoxide radical ; iron metabolism ; oxidative stress ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	500
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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