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  1. Article ; Online: Structural investigations of the palmitoylated F13 envelope protein of Mpox virus.

    Borkotoky, Subhomoi / Dey, Debajit

    Journal of medical virology

    2023  Volume 95, Issue 5, Page(s) e28798

    MeSH term(s) Monkeypox virus ; Viral Envelope Proteins/chemistry
    Chemical Substances Viral Envelope Proteins
    Language English
    Publishing date 2023-05-22
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.28798
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Structure-based drug designing against

    Sarma, Manash / Borkotoky, Subhomoi / Dubey, Vikash Kumar

    Journal of biomolecular structure & dynamics

    2023  , Page(s) 1–9

    Abstract: In the pursuit of developing novel anti-leishmanial agents, we conducted an extensive computational study to screen inhibitors from the FDA-approved ZINC database ... ...

    Abstract In the pursuit of developing novel anti-leishmanial agents, we conducted an extensive computational study to screen inhibitors from the FDA-approved ZINC database against
    Language English
    Publishing date 2023-07-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2240429
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    Zs.A 2093: Show issues Location:
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  3. Article ; Online: Interactions of angiotensin-converting enzyme-2 (ACE2) and SARS-CoV-2 spike receptor-binding domain (RBD): a structural perspective

    Borkotoky, Subhomoi / Dey, Debajit / Hazarika, Zaved

    Mol Biol Rep. 2023 Mar., v. 50, no. 3 p.2713-2721

    2023  

    Abstract: BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to ... ...

    Abstract BACKGROUND: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme-2 (ACE2) receptor, a critical component of the renin-angiotensin system (RAS) that initiates the viral transmission. Most of the critical mutations found in SARS-CoV-2 are associated with the RBD of the spike protein. These mutations have the potential to reduce the efficacy of vaccines and neutralizing antibodies. METHODS: In this review, the structural details of ACE2, RBD and their interactions are discussed. In addition, some critical mutations of RBD and their impact on ACE2-RBD interactions are also discussed. CONCLUSION: Preventing the interaction between Spike RBD and ACE2 is considered a viable therapeutic strategy since ACE2 binding by RBD is the first step in virus infection. Because the interactions between the two entities are critical for both viral transmission and therapeutic development, it is essential to understand their interactions in detail.
    Keywords Severe acute respiratory syndrome coronavirus 2 ; humans ; renin-angiotensin system ; therapeutics ; virus transmission ; viruses ; China
    Language English
    Dates of publication 2023-03
    Size p. 2713-2721.
    Publishing place Springer Netherlands
    Document type Article ; Online
    Note Review
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-022-08193-4
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  4. Article ; Online: The application of MD simulation to lead identification, vaccine design, and structural studies in combat against leishmaniasis - A review.

    Vijayakumar, Saravanan / Laxman Kumar, Lukkani / Borkotoky, Subhomoi / Murali, Ayaluru

    Mini reviews in medicinal chemistry

    2023  

    Abstract: Drug discovery, vaccine design, and protein interaction studies are rapidly moving toward the routine use of molecular dynamics simulations (MDS) and related methods. As a result of MDS, it is possible to gain insights into the dynamics and function of ... ...

    Abstract Drug discovery, vaccine design, and protein interaction studies are rapidly moving toward the routine use of molecular dynamics simulations (MDS) and related methods. As a result of MDS, it is possible to gain insights into the dynamics and function of identified drug targets, antibody-antigen interactions, potential vaccine candidates, intrinsically disordered proteins, and essential proteins. The MDS appears to be used in all possible ways in combating diseases such as cancer, however, it has not been well documented as to how effectively it is applied to infectious diseases such as Leishmaniasis. As a result, this systematic review aims to survey the application of MDS in combating leishmaniasis. We have systematically collected articles that illustrate the implementation of MDS in drug discovery, vaccine development, and structural studies related to Leishmaniasis. Of all the articles reviewed, we identified that only a limited number of studies focused on the development of vaccines against Leishmaniasis through MDS. Also, the PCA and FEL studies were not carried out in most of the studies. These two were globally accepted utilities to understand the conformational changes and hence it is recommended that this analysis should be taken up in similar approaches in the future.
    Language English
    Publishing date 2023-09-01
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2104081-3
    ISSN 1875-5607 ; 1389-5575
    ISSN (online) 1875-5607
    ISSN 1389-5575
    DOI 10.2174/1389557523666230901105231
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  5. Article ; Online: Targeting two potential sites of SARS-CoV-2 main protease through computational drug repurposing.

    Prakash, Archisha / Borkotoky, Subhomoi / Dubey, Vikash Kumar

    Journal of biomolecular structure & dynamics

    2022  Volume 41, Issue 7, Page(s) 3014–3024

    Abstract: Before the rise of SARS-CoV-2, emergence of different coronaviruses such as SARS-CoV and MERS-CoV has been reported that indicates possibility of the future novel pathogen from the coronavirus family at a pandemic level. In this context, explicit studies ...

    Abstract Before the rise of SARS-CoV-2, emergence of different coronaviruses such as SARS-CoV and MERS-CoV has been reported that indicates possibility of the future novel pathogen from the coronavirus family at a pandemic level. In this context, explicit studies on identifying inhibitors focused on the coronavirus life cycle, are immensely important. The main protease is critical for the life cycle of coronaviruses. Majority of the work done on the inhibitor studies on the catalytically active dimeric SARS-CoV-2 main protease (M
    MeSH term(s) Humans ; SARS-CoV-2 ; Antiviral Agents/pharmacology ; COVID-19 ; Protease Inhibitors/pharmacology ; Drug Repositioning/methods ; Molecular Docking Simulation ; Molecular Dynamics Simulation
    Chemical Substances Antiviral Agents ; Protease Inhibitors ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-)
    Language English
    Publishing date 2022-03-10
    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 10.1080/07391102.2022.2044907
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Interactions of angiotensin-converting enzyme-2 (ACE2) and SARS-CoV-2 spike receptor-binding domain (RBD): a structural perspective.

    Borkotoky, Subhomoi / Dey, Debajit / Hazarika, Zaved

    Molecular biology reports

    2022  Volume 50, Issue 3, Page(s) 2713–2721

    Abstract: Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to ... ...

    Abstract Background: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme-2 (ACE2) receptor, a critical component of the renin-angiotensin system (RAS) that initiates the viral transmission. Most of the critical mutations found in SARS-CoV-2 are associated with the RBD of the spike protein. These mutations have the potential to reduce the efficacy of vaccines and neutralizing antibodies.
    Methods: In this review, the structural details of ACE2, RBD and their interactions are discussed. In addition, some critical mutations of RBD and their impact on ACE2-RBD interactions are also discussed.
    Conclusion: Preventing the interaction between Spike RBD and ACE2 is considered a viable therapeutic strategy since ACE2 binding by RBD is the first step in virus infection. Because the interactions between the two entities are critical for both viral transmission and therapeutic development, it is essential to understand their interactions in detail.
    MeSH term(s) Humans ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; Angiotensins/metabolism ; Binding Sites ; COVID-19 ; Protein Binding/genetics ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/genetics
    Chemical Substances Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Angiotensins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23)
    Language English
    Publishing date 2022-12-23
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-022-08193-4
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    Zs.A 1140: Show issues Location:
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  7. Article ; Online: A computational prediction of SARS-CoV-2 structural protein inhibitors from

    Borkotoky, Subhomoi / Banerjee, Manidipa

    Journal of biomolecular structure & dynamics

    2020  Volume 39, Issue 11, Page(s) 4111–4121

    Abstract: The rapid global spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has created an unprecedented healthcare crisis. The treatment for the severe respiratory illness caused by this virus is primarily symptomatic at this point, ... ...

    Abstract The rapid global spread of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has created an unprecedented healthcare crisis. The treatment for the severe respiratory illness caused by this virus is primarily symptomatic at this point, although the usage of a broad antiviral drug Remdesivir has been allowed on emergency basis by the Food and Drug Administration (FDA). The ever-increasing death toll highlights an urgent need for development of specific antivirals. In this work, we have utilized docking and simulation methods to identify small molecule inhibitors of SARS-CoV-2 Membrane (M) and Envelope (E) proteins, which are essential for virus assembly and budding. A total of 70 compounds from an Indian medicinal plant source (
    MeSH term(s) Azadirachta ; COVID-19 ; Humans ; Molecular Docking Simulation ; Protease Inhibitors ; SARS-CoV-2
    Chemical Substances Protease Inhibitors
    Keywords covid19
    Language English
    Publishing date 2020-06-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2020.1774419
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Unravelling viral dynamics through molecular dynamics simulations - A brief overview.

    Borkotoky, Subhomoi / Dey, Debajit / Hazarika, Zaved / Joshi, Amit / Tripathi, Keshawanand

    Biophysical chemistry

    2022  Volume 291, Page(s) 106908

    Abstract: Viruses are a class of complex and dynamic macromolecular machines that can virtually infect all known life forms in the biosphere. This remarkable complexity results from a unique organization involving protein (capsid) and nucleic acid (DNA/RNA). A ... ...

    Abstract Viruses are a class of complex and dynamic macromolecular machines that can virtually infect all known life forms in the biosphere. This remarkable complexity results from a unique organization involving protein (capsid) and nucleic acid (DNA/RNA). A virus structure is metastable and highly responsive to environmental changes. Although major events of a virus life cycle are well characterized, several important questions with respect to how the nucleocapsid assemble/disassemble remain to be explored. In recent years due to enhanced computational power, molecular dynamics (MD) simulations have become an attractive alternative for addressing these questions since it is challenging to probe dynamic behavior with in vitro experimentation. The ability to simulate a complete virus particle provides an unprecedented atomic level resolution which can be used to understand its behavior under specific conditions. The current review outlines contributions made by all-atom and coarse-grained MD simulations towards understanding the mechanics and dynamics of virus structure and function. Databases and programs which facilitate such in silico investigations have also been discussed.
    MeSH term(s) Molecular Dynamics Simulation ; Proteins ; RNA ; Viruses ; DNA
    Chemical Substances Proteins ; RNA (63231-63-0) ; DNA (9007-49-2)
    Language English
    Publishing date 2022-10-12
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 185052-0
    ISSN 1873-4200 ; 0301-4622
    ISSN (online) 1873-4200
    ISSN 0301-4622
    DOI 10.1016/j.bpc.2022.106908
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    Zs.A 1147: Show issues Location:
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  9. Article ; Online: MERS virus spike protein HTL-epitopes selection and multi-epitope vaccine design using computational biology.

    Joshi, Amit / Akhtar, Nahid / Sharma, Neeta Raj / Kaushik, Vikas / Borkotoky, Subhomoi

    Journal of biomolecular structure & dynamics

    2023  Volume 41, Issue 22, Page(s) 12464–12479

    Abstract: MERS-CoV, a zoonotic virus, poses a serious threat to public health globally. Thus, it is imperative to develop an effective vaccination strategy for protection against MERS-CoV. Immunoinformatics and computational biology tools provide a faster and more ...

    Abstract MERS-CoV, a zoonotic virus, poses a serious threat to public health globally. Thus, it is imperative to develop an effective vaccination strategy for protection against MERS-CoV. Immunoinformatics and computational biology tools provide a faster and more cost-effective strategy to design potential vaccine candidates. In this work, the spike proteins from different strains of MERS-CoV were selected to predict HTL-epitopes that show affinity for T-helper MHC-class II HTL allelic determinant (HLA-DRB1:0101). The antigenicity and conservation of these epitopes among the selected spike protein variants in different MERS-CoV strains were analyzed. The analysis identified five epitopes with high antigenicity: QSIFYRLNGVGITQQ, DTIKYYSIIPHSIRS, PEPITSLNTKYVAPQ, INGRLTTLNAFVAQQ and GDMYVYSAGHATGTT. Then, a multi-epitope vaccine candidate was designed using linkers and adjuvant molecules. Finally, the vaccine construct was subjected to molecular docking with TLR5 (Toll-like receptor-5). The proposed vaccine construct had strong binding energy of -32.3 kcal/mol when interacting with TLR5.Molecular dynamics simulation analysis showed that the complex of the vaccine construct and TLR5 is stable. Analysis using
    MeSH term(s) Middle East Respiratory Syndrome Coronavirus/genetics ; Middle East Respiratory Syndrome Coronavirus/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Molecular Docking Simulation ; Toll-Like Receptor 5 ; Prospective Studies ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Viral Vaccines/chemistry ; Molecular Dynamics Simulation ; Vaccine Development ; Computational Biology ; Vaccines, Subunit
    Chemical Substances Spike Glycoprotein, Coronavirus ; Toll-Like Receptor 5 ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; Viral Vaccines ; Vaccines, Subunit
    Language English
    Publishing date 2023-03-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2191137
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2093: Show issues Location:
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  10. Article ; Online: Computational Insight Into the Mechanism of SARS-CoV-2 Membrane Fusion.

    Borkotoky, Subhomoi / Dey, Debajit / Banerjee, Manidipa

    Journal of chemical information and modeling

    2021  Volume 61, Issue 1, Page(s) 423–431

    Abstract: Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded ... ...

    Abstract Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded glycoproteins and are typically conserved within virus families. Here, we attempted to identify the correct fusion peptide region in the Spike protein of SARS-CoV-2 by all-atom molecular dynamics simulations of dual membrane systems with varied oligomeric units of putative candidate peptides. Of all of the systems tested, only a trimeric unit of a 40-amino-acid region (residues 816-855 of SARS-CoV-2 Spike) was effective in triggering the initial stages of membrane fusion, within 200 ns of simulation time. Association of this trimeric unit with dual membranes resulted in the migration of lipids from the upper leaflet of the lower bilayer toward the lower leaflet of the upper bilayer to create a structural unit reminiscent of a fusion bridge. We submit that residues 816-855 of Spike represent the bona fide fusion peptide of SARS-CoV-2 and that computational methods represent an effective way to identify fusion peptides in viral glycoproteins.
    MeSH term(s) Amino Acid Sequence ; COVID-19/metabolism ; COVID-19/virology ; Host-Pathogen Interactions ; Humans ; Membrane Fusion ; Molecular Dynamics Simulation ; Peptides/chemistry ; Peptides/metabolism ; Protein Multimerization ; SARS-CoV-2/chemistry ; SARS-CoV-2/physiology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Virus Internalization
    Chemical Substances Peptides ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2021-01-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.0c01231
    Database MEDical Literature Analysis and Retrieval System OnLINE

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