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  1. Article: Elucidating the Structural Features of ABCA1 in its Heterogeneous Membrane Environment.

    Sunidhi, S / Sacher, Sukriti / Atul / Garg, Parth / Ray, Arjun

    Frontiers in molecular biosciences

    2022  Volume 8, Page(s) 803078

    Abstract: ATP Binding Cassette Transporter A1 (ABCA1) plays an integral part in Reverse Cholesterol Transport (RCT) and is critical for maintaining lipid homeostasis. One theory of lipid efflux by the transporter (alternating access) proposes that ABCA1 harbours ... ...

    Abstract ATP Binding Cassette Transporter A1 (ABCA1) plays an integral part in Reverse Cholesterol Transport (RCT) and is critical for maintaining lipid homeostasis. One theory of lipid efflux by the transporter (alternating access) proposes that ABCA1 harbours two different conformations that provide alternating access for lipid binding and release. This is followed by sequestration
    Language English
    Publishing date 2022-01-27
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2021.803078
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum.

    Panda, Gayatri / Mishra, Neha / Sharma, Disha / Kutum, Rintu / Bhoyar, Rahul C / Jain, Abhinav / Imran, Mohamed / Senthilvel, Vigneshwar / Divakar, Mohit Kumar / Mishra, Anushree / Garg, Parth / Banerjee, Priyanka / Sivasubbu, Sridhar / Scaria, Vinod / Ray, Arjun

    Frontiers in pharmacology

    2022  Volume 13, Page(s) 858345

    Abstract: India confines more than 17% of the world's population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) ... ...

    Abstract India confines more than 17% of the world's population and has a diverse genetic makeup with several clinically relevant rare mutations belonging to many sub-group which are undervalued in global sequencing datasets like the 1000 Genome data (1KG) containing limited samples for Indian ethnicity. Such databases are critical for the pharmaceutical and drug development industry where diversity plays a crucial role in identifying genetic disposition towards adverse drug reactions. A qualitative and comparative sequence and structural study utilizing variant information present in the recently published, largest curated Indian genome database (IndiGen) and the 1000 Genome data was performed for variants belonging to the kinase coding genes, the second most targeted group of drug targets. The sequence-level analysis identified similarities and differences among different populations based on the nsSNVs and amino acid exchange frequencies whereas a comparative structural analysis of IndiGen variants was performed with pathogenic variants reported in UniProtKB Humsavar data. The influence of these variations on structural features of the protein, such as structural stability, solvent accessibility, hydrophobicity, and the hydrogen-bond network was investigated. In-silico screening of the known drugs to these Indian variation-containing proteins reveals critical differences imparted in the strength of binding due to the variations present in the Indian population. In conclusion, this study constitutes a comprehensive investigation into the understanding of common variations present in the second largest population in the world and investigating its implications in the sequence, structural and pharmacogenomic landscape. The preliminary investigation reported in this paper, supporting the screening and detection of ADRs specific to the Indian population could aid in the development of techniques for pre-clinical and post-market screening of drug-related adverse events in the Indian population.
    Language English
    Publishing date 2022-07-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2022.858345
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Transcriptome analysis and connectivity mapping of Cissampelos pareira L. provides molecular links of ESR1 modulation to viral inhibition.

    Haider, Madiha / Dholakia, Dhwani / Panwar, Aleksha / Garg, Parth / Gheware, Atish / Singh, Dayanidhi / Singhal, Khushboo / Burse, Shaunak A / Kumari, Surekha / Sharma, Anmol / Ray, Arjun / Medigeshi, Guruprasad R / Sharma, Upendra / Prasher, Bhavana / Mukerji, Mitali

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 20095

    Abstract: Bioactive fractions obtained from medicinal plants which have been used for the treatment of multiple diseases could exert their effects by targeting common pathways. Prior knowledge of their usage could allow us to identify novel molecular links. In ... ...

    Abstract Bioactive fractions obtained from medicinal plants which have been used for the treatment of multiple diseases could exert their effects by targeting common pathways. Prior knowledge of their usage could allow us to identify novel molecular links. In this study, we explored the molecular basis of action of one such herbal formulation Cissampelos pareira L. (Cipa), used for the treatment of female hormone disorders and fever. Transcriptomic studies on MCF7 cell lines treated with Cipa extract carried out using Affymetrix arrays revealed a downregulation of signatures of estrogen response potentially modulated through estrogen receptor α (ERα). Molecular docking analysis identified 38 Cipa constituents that potentially bind (ΔG <  - 7.5) with ERα at the same site as estrogen. The expression signatures in the connectivity map ( https://clue.io/; ) revealed high positive scores with translation inhibitors such as emetine (score: 99.61) and knockdown signatures of genes linked to the antiviral response such as ribosomal protein RPL7 (score: 99.92), which is a reported ERα coactivator. Further, gene knockdown experiments revealed that Cipa exhibits antiviral activity in dengue infected MCF7 cells potentially modulated through estrogen receptor 1. This approach reveals a novel pathway involving the ESR1-RPL7 axis which could be a potential target in dengue viral infection.
    MeSH term(s) Antiviral Agents/pharmacology ; Breast Neoplasms/drug therapy ; Breast Neoplasms/metabolism ; Breast Neoplasms/pathology ; Breast Neoplasms/virology ; Cissampelos/chemistry ; Dengue/drug therapy ; Dengue/metabolism ; Dengue/pathology ; Dengue/virology ; Dengue Virus ; Estrogen Receptor alpha/genetics ; Estrogen Receptor alpha/metabolism ; Female ; Humans ; MCF-7 Cells ; Plant Extracts/pharmacology ; Transcriptome/drug effects
    Chemical Substances Antiviral Agents ; ESR1 protein, human ; Estrogen Receptor alpha ; Plant Extracts
    Language English
    Publishing date 2021-10-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-021-99444-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry.

    Singh, Praveen / Chakraborty, Rahul / Marwal, Robin / Radhakrishan, V S / Bhaskar, Akash Kumar / Vashisht, Himanshu / Dhar, Mahesh S / Pradhan, Shalini / Ranjan, Gyan / Imran, Mohamed / Raj, Anurag / Sharma, Uma / Singh, Priyanka / Lall, Hemlata / Dutta, Meena / Garg, Parth / Ray, Arjun / Dash, Debasis / Sivasubbu, Sridhar /
    Gogia, Hema / Madan, Preeti / Kabra, Sandhya / Singh, Sujeet K / Agrawal, Anurag / Rakshit, Partha / Kumar, Pramod / Sengupta, Shantanu

    Journal of proteins and proteomics

    2020  Volume 11, Issue 3, Page(s) 159–165

    Abstract: In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the ... ...

    Abstract In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 min gradient run with 100% specificity and 90.5% sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.
    Keywords covid19
    Language English
    Publishing date 2020-08-31
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2890453-9
    ISSN 2524-4663 ; 0975-8151
    ISSN (online) 2524-4663
    ISSN 0975-8151
    DOI 10.1007/s42485-020-00044-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Traditional use of Cissampelos pareira L. for hormone disorder and fever provides molecular links of ESR1 modulation to viral inhibition

    Haider, Madiha / Dholakia, Dhwani / Panwar, Aleksha / Garg, Parth / Anand, Vivek / Gheware, Atish Prabhakar / Singhal, Khushboo / Singh, Dayanidhi / Burse, Shaunak A / Enayathullah, M Ghalib / Parekh, Yash / Ram, Sushma / Kumari, Surekha / Kumar, Anmol / Ray, Arjun / Medigeshi, Guruprasad R / Bokara, Kiran Kumar / Sharma, Upendra / Prasher, Bhavana /
    Mukerji, Mitali

    bioRxiv

    Abstract: In traditional systems, a single herbal formulation is often used in the treatment of diverse diseases, including some that are newly emergent and prevalent today. We provide here a multi-omics framework to probe the molecular basis of a multicomponent ... ...

    Abstract In traditional systems, a single herbal formulation is often used in the treatment of diverse diseases, including some that are newly emergent and prevalent today. We provide here a multi-omics framework to probe the molecular basis of a multicomponent example herb, Cissampelos pareira L. (Cipa) used in the treatment of hormonal disorders and fever in Ayurveda. Cipa treated MCF7 cells exhibit downregulation of signatures of estrogen response. 38 constituent molecules in Cipa potentially bind (∆G< -7.5) with ERα at the same site as estrogen. Cipa transcriptome signatures in the connectivity map exhibit positive scores with protein translation inhibitors and knockdown signatures of genes linked to the antiviral response. This includes the knockdown signature of RPL7, a coactivator of ESRI with a connectivity score > 99.69. This axis was found to be upregulated in the COVID-19 patient transcriptome. The antiviral activity through ESR1 modulation was validated in the DENV-2 infection model. We further observed 98% inhibition of SARs-COV-2 replication in infected Vero cell cultures with the whole extract. A few of its prominent pure constituents e.g pareirarine, cissamine, magnoflorine exhibited 40-80% inhibition. This study provides a novel framework for querying the molecular links of multicomponent Ayurveda formulations and explains their use in the treatment of disparate diseases. The novel biological targets identified here can become potential that could be applicable to more than one viral infection, such as the use of Cipa in dengue and COVID-19.
    Keywords covid19
    Language English
    Publishing date 2021-02-17
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.02.17.431579
    Database COVID19

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  6. Article ; Online: A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry

    Singh, Praveen / Chakraborty, Rahul / Marwal, Robin / V S, Radhakrishan / Bhaskar, Akash Kumar / Vashisht, Himanshu / Dhar, Mahesh S / Pradhan, Shalini / Ranjan, Gyan / Imran, Mohamed / Raj, Anurag / Sharma, Uma / Singh, Priyanka / Lall, Hemlata / Dutta, Meena / Garg, Parth / Ray, Arjun / Dash, Debasis / Sivasubbu, Sridhar /
    Gogia, Hema / Madan, Preeti / Kabra, Sandhya / Singh, Sujeet K / Agrawal, Anurag / Rakhit, Partha / Kumar, Pramod / Sengupta, Shantanu

    medRxiv

    Abstract: In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel corona virus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation is key to contain the ... ...

    Abstract In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel corona virus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation is key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 minute gradient run with 100% specificity and 90.4 % sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.
    Keywords covid19
    Language English
    Publishing date 2020-07-29
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.07.27.20161836
    Database COVID19

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  7. Article: A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry

    Singh, Praveen / Chakraborty, Rahul / Marwal, Robin / Radhakrishan, V S / Bhaskar, Akash Kumar / Vashisht, Himanshu / Dhar, Mahesh S / Pradhan, Shalini / Ranjan, Gyan / Imran, Mohamed / Raj, Anurag / Sharma, Uma / Singh, Priyanka / Lall, Hemlata / Dutta, Meena / Garg, Parth / Ray, Arjun / Dash, Debasis / Sivasubbu, Sridhar /
    Gogia, Hema / Madan, Preeti / Kabra, Sandhya / Singh, Sujeet K / Agrawal, Anurag / Rakshit, Partha / Kumar, Pramod / Sengupta, Shantanu

    J Proteins Proteom

    Abstract: In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the ... ...

    Abstract In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 min gradient run with 100% specificity and 90.5% sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #747107
    Database COVID19

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  8. Article ; Online: A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry

    Singh, Praveen / Chakraborty, Rahul / Marwal, Robin / Radhakrishan, V. S. / Bhaskar, Akash Kumar / Vashisht, Himanshu / Dhar, Mahesh S. / Pradhan, Shalini / Ranjan, Gyan / Imran, Mohamed / Raj, Anurag / Sharma, Uma / Singh, Priyanka / Lall, Hemlata / Dutta, Meena / Garg, Parth / Ray, Arjun / Dash, Debasis / Sivasubbu, Sridhar /
    Gogia, Hema / Madan, Preeti / Kabra, Sandhya / Singh, Sujeet K. / Agrawal, Anurag / Rakshit, Partha / Kumar, Pramod / Sengupta, Shantanu

    Journal of Proteins and Proteomics

    2020  Volume 11, Issue 3, Page(s) 159–165

    Keywords covid19
    Language English
    Publisher Springer Science and Business Media LLC
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2890453-9
    ISSN 2524-4663 ; 0975-8151
    ISSN (online) 2524-4663
    ISSN 0975-8151
    DOI 10.1007/s42485-020-00044-9
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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