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  1. Article ; Online: Advances in Drug Discovery based on Genomics, Proteomics and Bioinformatics in Malaria.

    Aggarwal, Shalini / Karmakar, Amit / Krishnakumar, Sanjana / Paul, Utpalendu / Singh, Anjali / Banerjee, Nirjhar / Laha, Nehashri / Roy Ball, Graham / Srivastava, Sanjeeva

    Current topics in medicinal chemistry

    2023  Volume 23, Issue 7, Page(s) 551–578

    Abstract: Malaria is one of the neglected infectious diseases, and drugs are the first line of action taken against the onset of malaria as therapeutics. The drugs can be of either natural or artificial origin. Drug development has multiple impediments grouped ... ...

    Abstract Malaria is one of the neglected infectious diseases, and drugs are the first line of action taken against the onset of malaria as therapeutics. The drugs can be of either natural or artificial origin. Drug development has multiple impediments grouped under three categories, a. drug discovery and screening, b. the drug's action on the host and the pathogen, and c. clinical trials. Drug development takes coon's age from discovery to the market after FDA approval. At the same time, targeted organisms develop drug resistance quicker than drug approval, raising the requirement for advancement in drug development. The approach to explore drug candidates using the classical methods from natural sources, computation-based docking, mathematical and machine learningbased high throughput in silico models or drug repurposing has been investigated and developed. Also, drug development with information about the interaction between Plasmodium species and its host, humans, may facilitate obtaining an efficient drug cohort for further drug discovery or repurposing expedition. However, drugs may have side effects on the host system. Hence, machine learning and systems-based approaches may provide a holistic view of genomic, proteomic, and transcriptomic data and their interaction with the selected drug candidates. This review comprehensively describes the drug discovery workflows using drug and target screening methodologies, followed by possible ways to check the binding affinity of the drug and targets using various docking software.
    MeSH term(s) Humans ; Proteomics ; Genomics ; Computational Biology ; Drug Discovery ; Malaria/drug therapy ; Drug Repositioning
    Language English
    Publishing date 2023-04-19
    Publishing country United Arab Emirates
    Document type Review ; Journal Article
    ZDB-ID 2064823-6
    ISSN 1873-4294 ; 1568-0266
    ISSN (online) 1873-4294
    ISSN 1568-0266
    DOI 10.2174/1568026623666230418114455
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients.

    Suvarna, Kruthi / Salkar, Akanksha / Palanivel, Viswanthram / Bankar, Renuka / Banerjee, Nirjhar / Gayathri J Pai, Medha / Srivastava, Alisha / Singh, Avinash / Khatri, Harsh / Agrawal, Sachee / Shrivastav, Om / Shastri, Jayanthi / Srivastava, Sanjeeva

    Journal of proteome research

    2021  Volume 20, Issue 10, Page(s) 4667–4680

    Abstract: Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with fatality in severe infections. However, the specific ... ...

    Abstract Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with fatality in severe infections. However, the specific molecular signatures associated with the elevated immune response are yet to be elucidated. We performed a mass-spectrometry-based proteomic and metabolomic analysis of COVID-19 plasma samples collected at two time points. Using Orbitrap Fusion LC-MS/MS-based label-free proteomic analysis, we identified around 10 significant proteins, 32 significant peptides, and 5 metabolites that were dysregulated at the severe time points. Few of these proteins identified by quantitative proteomics were validated using the multiple reaction monitoring (MRM) assay. Integrated pathway analysis using distinct proteomic and metabolomic signatures revealed alterations in complement and coagulation cascade, platelet aggregation, myeloid leukocyte activation pathway, and arginine metabolism. Further, we highlight the role of leukocyte activation and arginine metabolism in COVID-19 pathogenesis and targeting these pathways for COVID-19 therapeutics.
    MeSH term(s) COVID-19 ; Chromatography, Liquid ; Humans ; Leukocytes ; Longitudinal Studies ; Proteomics ; SARS-CoV-2 ; Tandem Mass Spectrometry
    Language English
    Publishing date 2021-08-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.1c00215
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 6189: Show issues Location:
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  3. Article: A Multi-omics Longitudinal Study Reveals Alteration of the Leukocyte Activation Pathway in COVID-19 Patients

    Suvarna, Kruthi / Salkar, Akanksha / Palanivel, Viswanthram / Bankar, Renuka / Banerjee, Nirjhar / Gayathri J Pai, Medha / Srivastava, Alisha / Singh, Avinash / Khatri, Harsh / Agrawal, Sachee / Shrivastav, Om / Shastri, Jayanthi / Srivastava, Sanjeeva

    Journal of proteome research. 2021 Aug. 11, v. 20, no. 10

    2021  

    Abstract: Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with fatality in severe infections. However, the specific ... ...

    Abstract Severe coronavirus disease 2019 (COVID-19) infection may lead to lung injury, multi-organ failure, and eventually death. Cytokine storm due to excess cytokine production has been associated with fatality in severe infections. However, the specific molecular signatures associated with the elevated immune response are yet to be elucidated. We performed a mass-spectrometry-based proteomic and metabolomic analysis of COVID-19 plasma samples collected at two time points. Using Orbitrap Fusion LC–MS/MS-based label-free proteomic analysis, we identified around 10 significant proteins, 32 significant peptides, and 5 metabolites that were dysregulated at the severe time points. Few of these proteins identified by quantitative proteomics were validated using the multiple reaction monitoring (MRM) assay. Integrated pathway analysis using distinct proteomic and metabolomic signatures revealed alterations in complement and coagulation cascade, platelet aggregation, myeloid leukocyte activation pathway, and arginine metabolism. Further, we highlight the role of leukocyte activation and arginine metabolism in COVID-19 pathogenesis and targeting these pathways for COVID-19 therapeutics.
    Keywords COVID-19 infection ; arginine ; coagulation ; complement ; cytokines ; death ; immune response ; leukocytes ; longitudinal studies ; lungs ; metabolism ; metabolites ; metabolomics ; multiomics ; pathogenesis ; platelet aggregation ; proteome ; proteomics ; research ; therapeutics
    Language English
    Dates of publication 2021-0811
    Size p. 4667-4680.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 2078618-9
    ISSN 1535-3907 ; 1535-3893
    ISSN (online) 1535-3907
    ISSN 1535-3893
    DOI 10.1021/acs.jproteome.1c00215
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 6189: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: FAIR: A server for internal sequence repeats.

    Senthilkumar, Ramaswamy / Sabarinathan, Radhakrishnan / Hameed, Bazil Shaahul / Banerjee, Nirjhar / Chidambarathanu, Narayanan / Karthik, Rajadurai / Sekar, Kanagaraj

    Bioinformation

    2010  Volume 4, Issue 7, Page(s) 271–275

    Abstract: Unlabelled: An Internet computing server has been developed to identify all the occurrences of the internal sequence repeats in a protein and DNA sequences. Further, an option is provided for the users to check the occurrence(s) of the resultant ... ...

    Abstract Unlabelled: An Internet computing server has been developed to identify all the occurrences of the internal sequence repeats in a protein and DNA sequences. Further, an option is provided for the users to check the occurrence(s) of the resultant sequence repeats in the other sequence and structure (Protein Data Bank) databases. The databases deployed in the proposed computing engine are up-to-date and thus the users will get the latest information available in the respective databases. The server is freely accessible over the World Wide Web (WWW).
    Availability: http://bioserver1.physics.iisc.ernet.in/fair/
    Language English
    Publishing date 2010-01-07
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063 ; 0973-2063
    ISSN (online) 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630004271
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Algorithm to find distant repeats in a single protein sequence.

    Banerjee, Nirjhar / Sarani, Rangarajan / Ranjani, Chellamuthu Vasuki / Sowmiya, Govindaraj / Michael, Daliah / Balakrishnan, Narayanasamy / Sekar, Kanagaraj

    Bioinformation

    2008  Volume 3, Issue 1, Page(s) 28–32

    Abstract: Distant repeats in protein sequence play an important role in various aspects of protein analysis. A keen analysis of the distant repeats would enable to establish a firm relation of the repeats with respect to their function and three-dimensional ... ...

    Abstract Distant repeats in protein sequence play an important role in various aspects of protein analysis. A keen analysis of the distant repeats would enable to establish a firm relation of the repeats with respect to their function and three-dimensional structure during the evolutionary process. Further, it enlightens the diversity of duplication during the evolution. To this end, an algorithm has been developed to find all distant repeats in a protein sequence. The scores from Point Accepted Mutation (PAM) matrix has been deployed for the identification of amino acid substitutions while detecting the distant repeats. Due to the biological importance of distant repeats, the proposed algorithm will be of importance to structural biologists, molecular biologists, biochemists and researchers involved in phylogenetic and evolutionary studies.
    Language English
    Publishing date 2008-09-19
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063 ; 0973-2063
    ISSN (online) 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630003028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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