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  1. Article ; Online: Methodological advances in the design of peptide-based vaccines.

    Kalita, Parismita / Tripathi, Timir

    Drug discovery today

    2022  Volume 27, Issue 5, Page(s) 1367–1380

    Abstract: The tremendous advances in genomics, recombinant DNA technology, bioengineering and nanotechnology, in conjunction with the development of high-end computations, have been instrumental in the process of rational design of peptide-based vaccines. The use ... ...

    Abstract The tremendous advances in genomics, recombinant DNA technology, bioengineering and nanotechnology, in conjunction with the development of high-end computations, have been instrumental in the process of rational design of peptide-based vaccines. The use of peptide vaccines was limited owing to their inherent instability when systemically administered; however, advanced formulation techniques have been developed for their systemic delivery, thereby overcoming their degradation, clearance, cellular uptake and off-target effects. With the rise of sophisticated immunological predictors and experimental techniques, several methodological advances have occurred in this field. This review examines contemporary methods to identify and optimize epitopes, engineer their immunogenic properties and develop their safe and efficient delivery into the host.
    MeSH term(s) Computational Biology/methods ; Epitopes ; Epitopes, T-Lymphocyte/genetics ; Peptides ; Vaccines, Subunit
    Chemical Substances Epitopes ; Epitopes, T-Lymphocyte ; Peptides ; Vaccines, Subunit
    Language English
    Publishing date 2022-03-10
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1324988-5
    ISSN 1878-5832 ; 1359-6446
    ISSN (online) 1878-5832
    ISSN 1359-6446
    DOI 10.1016/j.drudis.2022.03.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Computational Protein Design for COVID-19 Research and Emerging Therapeutics.

    Kalita, Parismita / Tripathi, Timir / Padhi, Aditya K

    ACS central science

    2023  Volume 9, Issue 4, Page(s) 602–613

    Abstract: As the world struggles with the ongoing COVID-19 pandemic, unprecedented obstacles have continuously been traversed as new SARS-CoV-2 variants continually emerge. Infectious disease outbreaks are unavoidable, but the knowledge gained from the successes ... ...

    Abstract As the world struggles with the ongoing COVID-19 pandemic, unprecedented obstacles have continuously been traversed as new SARS-CoV-2 variants continually emerge. Infectious disease outbreaks are unavoidable, but the knowledge gained from the successes and failures will help create a robust health management system to deal with such pandemics. Previously, scientists required years to develop diagnostics, therapeutics, or vaccines; however, we have seen that, with the rapid deployment of high-throughput technologies and unprecedented scientific collaboration worldwide, breakthrough discoveries can be accelerated and insights broadened. Computational protein design (CPD) is a game-changing new technology that has provided alternative therapeutic strategies for pandemic management. In addition to the development of peptide-based inhibitors, miniprotein binders, decoys, biosensors, nanobodies, and monoclonal antibodies, CPD has also been used to redesign native SARS-CoV-2 proteins and human ACE2 receptors. We discuss how novel CPD strategies have been exploited to develop rationally designed and robust COVID-19 treatment strategies.
    Language English
    Publishing date 2023-03-20
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2374-7943
    ISSN 2374-7943
    DOI 10.1021/acscentsci.2c01513
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  3. Article ; Online: Immunoinformatics Protocol to Design Multi-Epitope Subunit Vaccines.

    Kalita, Parismita / Padhi, Aditya K / Tripathi, Timir

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2673, Page(s) 357–369

    Abstract: With the development of scientific technologies, the accessibility of genomic data, computational tools, software, databases, and machine learning, the field of immunoinformatics has emerged as an effective technique for immunologists to design potential ...

    Abstract With the development of scientific technologies, the accessibility of genomic data, computational tools, software, databases, and machine learning, the field of immunoinformatics has emerged as an effective technique for immunologists to design potential vaccines in a short time. A large number of tools and databases are available to screen the genome sequences of parasites/pathogens and identify the highly immunogenic peptides or epitopes that can be used to design effective vaccines. In this chapter, we provide an easy-to-use protocol for the design of multi-epitope-based subunit vaccines. Though the computational immunoinformatics-based approaches have demonstrated their competency in designing potentially effective vaccine candidates quickly, their immunogenicity and safety must be evaluated in laboratory settings before they are tested in clinical trials.
    MeSH term(s) Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Vaccines, Subunit ; Peptides ; Computational Biology/methods ; Molecular Docking Simulation
    Chemical Substances Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Vaccines, Subunit ; Peptides
    Language English
    Publishing date 2023-05-31
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3239-0_25
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Enabling Ultrahigh Surface Area of Covalently-linked Organic Framework for Boosted CO

    Jyoti Bora, Hridoy / Jyoti Boruah, Palash / Kalita, Parismita / Gogoi, Gautomi / Bailung, Heremba / Sen Sarma, Neelotpal / Kalita, Anamika

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2023  Volume 29, Issue 38, Page(s) e202300756

    Abstract: The cognitive intent of a highly ordered and robust adsorbent is extremely sensible and, in this context, Covalent Organic Framework (COF) materials have significantly burgeoned their scope in diverse applications. Herein, a simple time-competent ... ...

    Abstract The cognitive intent of a highly ordered and robust adsorbent is extremely sensible and, in this context, Covalent Organic Framework (COF) materials have significantly burgeoned their scope in diverse applications. Herein, a simple time-competent hydrothermal procedure is presented to construct a covalent framework with an ultrahigh surface area of 1428 m
    MeSH term(s) Carbon Dioxide ; Adsorption ; Biological Transport ; Metal-Organic Frameworks ; Software
    Chemical Substances Carbon Dioxide (142M471B3J) ; Metal-Organic Frameworks
    Language English
    Publishing date 2023-05-11
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1478547-X
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.202300756
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: From

    Padhi, Aditya K / Kalita, Parismita / Maurya, Shweata / Poluri, Krishna Mohan / Tripathi, Timir

    The journal of physical chemistry. B

    2023  Volume 127, Issue 41, Page(s) 8717–8735

    Abstract: The continuous emergence of novel SARS-CoV-2 variants and subvariants serves as compelling evidence that COVID-19 is an ongoing concern. The swift, well-coordinated response to the pandemic highlights how technological advancements can accelerate the ... ...

    Abstract The continuous emergence of novel SARS-CoV-2 variants and subvariants serves as compelling evidence that COVID-19 is an ongoing concern. The swift, well-coordinated response to the pandemic highlights how technological advancements can accelerate the detection, monitoring, and treatment of the disease. Robust surveillance systems have been established to understand the clinical characteristics of new variants, although the unpredictable nature of these variants presents significant challenges. Some variants have shown resistance to current treatments, but innovative technologies like computational protein design (CPD) offer promising solutions and versatile therapeutics against SARS-CoV-2. Advances in computing power, coupled with open-source platforms like AlphaFold and RFdiffusion (employing deep neural network and diffusion generative models), among many others, have accelerated the design of protein therapeutics with precise structures and intended functions. CPD has played a pivotal role in developing peptide inhibitors, mini proteins, protein mimics, decoy receptors, nanobodies, monoclonal antibodies, identifying drug-resistance mutations, and even redesigning native SARS-CoV-2 proteins. Pending regulatory approval, these designed therapies hold the potential for a lasting impact on human health and sustainability. As SARS-CoV-2 continues to evolve, use of such technologies enables the ongoing development of alternative strategies, thus equipping us for the "New Normal".
    MeSH term(s) Humans ; SARS-CoV-2 ; COVID-19/therapy ; Antibodies, Monoclonal ; Diffusion
    Chemical Substances Antibodies, Monoclonal
    Language English
    Publishing date 2023-10-10
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c04542
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Functional expression, localization, and biochemical characterization of thioredoxin glutathione reductase from air-breathing magur catfish, Clarias magur.

    Koner, Debaprasad / Nag, Niharika / Kalita, Parismita / Padhi, Aditya K / Tripathi, Timir / Saha, Nirmalendu

    International journal of biological macromolecules

    2023  Volume 230, Page(s) 123126

    Abstract: The glutathione (GSH) and thioredoxin (Trx) systems regulate cellular redox homeostasis and maintain antioxidant defense in most eukaryotes. We earlier reported the absence of gene coding for the glutathione reductase (GR) enzyme of the GSH system in the ...

    Abstract The glutathione (GSH) and thioredoxin (Trx) systems regulate cellular redox homeostasis and maintain antioxidant defense in most eukaryotes. We earlier reported the absence of gene coding for the glutathione reductase (GR) enzyme of the GSH system in the facultative air-breathing catfish, Clarias magur. Here, we identified three thioredoxin reductase (TrxR) genes, one of which was later confirmed as a thioredoxin glutathione reductase (TGR). We then characterized the novel recombinant TGR enzyme of C. magur (CmTGR). The tissue-specific expression of the txnrd genes and the tissue-specific activity of the TrxR enzyme were analyzed. The recombinant CmTGR is a dimer of ~133 kDa. The protein showed TrxR activity with 5,5'-diothiobis (2-nitrobenzoic acid) reduction assay with a K
    MeSH term(s) Animals ; Catfishes/genetics ; Catfishes/metabolism ; Phylogeny ; Platyhelminths ; Glutathione/metabolism ; Antioxidants ; Thioredoxin-Disulfide Reductase/genetics ; Thioredoxins/genetics ; Glutathione Reductase/genetics
    Chemical Substances thioredoxin glutathione reductase (EC 1.6.4.-) ; Glutathione (GAN16C9B8O) ; Antioxidants ; Thioredoxin-Disulfide Reductase (EC 1.8.1.9) ; Thioredoxins (52500-60-4) ; Glutathione Reductase (EC 1.8.1.7)
    Language English
    Publishing date 2023-01-02
    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.2022.123126
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  7. Article ; Online: Unveiling the Potential of Covalent Organic Framework Electrocatalyst for Enhanced Oxygen Evolution.

    Bora, Hridoy Jyoti / Nath, Manash P / Medhi, Palash Jyoti / Boruah, Palash Jyoti / Kalita, Parismita / Bailung, Heremba / Choudhury, Biswajit / Sen Sarma, Neelotpal / Kalita, Anamika

    Langmuir : the ACS journal of surfaces and colloids

    2024  

    Abstract: The potential for sustainable energy and carbon neutrality has expanded with the development of a highly active electrocatalyst for the oxygen evolution reaction (OER). Covalent Organic Frameworks (COF) have recently garnered attention because of their ... ...

    Abstract The potential for sustainable energy and carbon neutrality has expanded with the development of a highly active electrocatalyst for the oxygen evolution reaction (OER). Covalent Organic Frameworks (COF) have recently garnered attention because of their enormous potential in a number of cutting-edge application sectors, such as gas storage, sensors, fuel cells, and active catalytic supports. A simple and effective COF constructed and integrated by post-alteration plasma modification facilitates high electrocatalytic OER activity under alkaline conditions. Variations in parameters such as voltage and treatment duration have been employed to enhance the factor that demonstrates high OER performance. The overpotential and Tafel slope are the lowest of all when using an optimized parameter, such as plasma treatment for 30 min utilizing 6 kV of voltage, PT-30 COF, measuring 390 mV at a current density of 10 mA.cm
    Language English
    Publishing date 2024-04-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2005937-1
    ISSN 1520-5827 ; 0743-7463
    ISSN (online) 1520-5827
    ISSN 0743-7463
    DOI 10.1021/acs.langmuir.4c00788
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  8. Article ; Online: Synergistic Effect of Amyloid-β and Tau Disrupts Neural Circuits.

    Tripathi, Timir / Kalita, Parismita

    ACS chemical neuroscience

    2019  Volume 10, Issue 3, Page(s) 1129–1130

    Abstract: Alzheimer's disease (AD) is characterized by the coexistence of amyloid-β (Aβ) plaques and tau-based neurofibrillary tangles. Although studies have shown that the interaction between Aβ and tau causes enhanced AD pathology; there is a lack of precise ... ...

    Abstract Alzheimer's disease (AD) is characterized by the coexistence of amyloid-β (Aβ) plaques and tau-based neurofibrillary tangles. Although studies have shown that the interaction between Aβ and tau causes enhanced AD pathology; there is a lack of precise understanding of the functional consequences for integrated neural circuits. A recent study revealed that the interaction between Aβ and tau pathologies impairs the functional integrity of neural circuits in the AD brain. Thus, not only Aβ but also tau determines the cognitive status. Therefore, developing anti-Aβ or anti-aggregated tau compounds may not be an effective strategy to treat AD. In fact, approaches combining anti-Aβ and anti-tau therapies might be a more promising therapeutic option rather than single therapy. The results have important therapeutic implications not only for AD but also for other tauopathies.
    MeSH term(s) Amyloid beta-Peptides/antagonists & inhibitors ; Amyloid beta-Peptides/genetics ; Amyloid beta-Peptides/metabolism ; Animals ; Genetic Therapy/trends ; Humans ; Nerve Net/metabolism ; Nerve Net/pathology ; Plaque, Amyloid/genetics ; Plaque, Amyloid/metabolism ; Plaque, Amyloid/pathology ; Tauopathies/genetics ; Tauopathies/metabolism ; Tauopathies/pathology ; tau Proteins/antagonists & inhibitors ; tau Proteins/genetics ; tau Proteins/metabolism
    Chemical Substances Amyloid beta-Peptides ; tau Proteins
    Language English
    Publishing date 2019-01-31
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 1948-7193
    ISSN (online) 1948-7193
    DOI 10.1021/acschemneuro.9b00037
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  9. Article ; Online: Functional expression, localization, and biochemical characterization of thioredoxin glutathione reductase from air-breathing magur catfish, Clarias magur

    Koner, Debaprasad / Nag, Niharika / Kalita, Parismita / Padhi, Aditya K. / Tripathi, Timir / Saha, Nirmalendu

    International Journal of Biological Macromolecules. 2023 Mar., v. 230 p.123126-

    2023  

    Abstract: The glutathione (GSH) and thioredoxin (Trx) systems regulate cellular redox homeostasis and maintain antioxidant defense in most eukaryotes. We earlier reported the absence of gene coding for the glutathione reductase (GR) enzyme of the GSH system in the ...

    Abstract The glutathione (GSH) and thioredoxin (Trx) systems regulate cellular redox homeostasis and maintain antioxidant defense in most eukaryotes. We earlier reported the absence of gene coding for the glutathione reductase (GR) enzyme of the GSH system in the facultative air-breathing catfish, Clarias magur. Here, we identified three thioredoxin reductase (TrxR) genes, one of which was later confirmed as a thioredoxin glutathione reductase (TGR). We then characterized the novel recombinant TGR enzyme of C. magur (CmTGR). The tissue-specific expression of the txnrd genes and the tissue-specific activity of the TrxR enzyme were analyzed. The recombinant CmTGR is a dimer of ~133 kDa. The protein showed TrxR activity with 5,5′-diothiobis (2-nitrobenzoic acid) reduction assay with a Kₘ of 304.40 μM and GR activity with a Kₘ of 58.91 μM. Phylogenetic analysis showed that the CmTGR was related to the TrxRs of fishes and distantly related to the TGRs of platyhelminth parasites. The structural analysis revealed the conserved glutaredoxin active site and FAD- and NADPH-binding sites. To our knowledge, this is the first report of the presence of a TGR in any fish. This unusual presence of TGR in C. magur is crucial as it helps maintain redox homeostasis under environmental stressors-induced oxidative stress.
    Keywords Clarias magur ; active sites ; antioxidant activity ; catfish ; eukaryotic cells ; genes ; glutathione ; glutathione-disulfide reductase ; homeostasis ; nitrobenzoic acids ; oxidative stress ; phylogeny ; thioredoxins ; Thioredoxin reductase ; Glutathione reductase ; Redox homeostasis ; Magur catfish ; Glutathione-glutathione disulfide pool
    Language English
    Dates of publication 2023-03
    Publishing place Elsevier B.V.
    Document type Article ; Online
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2022.123126
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  10. Article ; Online: Corrigendum to "Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2" [Microbial Pathog. 145 (2020) 104236].

    Kalita, Parismita / Padhi, Aditya K / Zhang, Kam Y J / Tripathi, Timir

    Microbial pathogenesis

    2020  Volume 160, Page(s) 104401

    Language English
    Publishing date 2020-07-20
    Publishing country England
    Document type Published Erratum
    ZDB-ID 632772-2
    ISSN 1096-1208 ; 0882-4010
    ISSN (online) 1096-1208
    ISSN 0882-4010
    DOI 10.1016/j.micpath.2020.104401
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