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  1. Article ; Online: Editorial: ESKAPE biofilm: challenges and solutions.

    Tiwari, Vishvanath

    Frontiers in cellular and infection microbiology

    2023  Volume 13, Page(s) 1253439

    Language English
    Publishing date 2023-08-01
    Publishing country Switzerland
    Document type Editorial
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2023.1253439
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Pharmacophore screening, denovo designing, retrosynthetic analysis, and combinatorial synthesis of a novel lead VTRA1.1 against RecA protein of Acinetobacter baumannii.

    Tiwari, Vishvanath

    Chemical biology & drug design

    2022  Volume 99, Issue 6, Page(s) 839–856

    Abstract: Antibiotics and disinfectants resistance is acquired by activating RecA-mediated DNA repair, which maintains ROS-dependent DNA damage caused by the antimicrobial molecules. To increase the efficacy of different antimicrobials, an inhibitor can be ... ...

    Abstract Antibiotics and disinfectants resistance is acquired by activating RecA-mediated DNA repair, which maintains ROS-dependent DNA damage caused by the antimicrobial molecules. To increase the efficacy of different antimicrobials, an inhibitor can be developed against RecA protein. The present study aims to design a denovo inhibitor against RecA protein of Acinetobacter baumannii. Pharmacophore-based screening, molecular mechanics, molecular dynamics simulation (MDS), retrosynthetic analysis, and combinatorial synthesis were used to design lead VTRA1.1 against RecA of A. baumannii. Pharmacophore models (structure-based and ligand-based) were created, and a phase library of FDA-approved drugs was prepared. Screening of the phase library against these pharmacophore models selected thirteen lead molecules. These filtered leads were used for the denovo fragment-based design, which produced 253 combinations. These designed molecules were further analyzed for its interaction with active site of RecA that selected a hybrid VTRA1. Further, retrosynthetic analysis and combinatorial synthesis produced 1000 analogs of VTRA1 by more than 100 modifications. These analogs were used for XP docking, binding free energy calculation, and MDS analysis which finally select lead VTRA1.1 against RecA protein. Further, mutations at the interacting residues of RecA with VTRA1.1, alter the unfolding rate of RecA, which suggests the binding of VTRA1.1 to these residues may alter the stability of RecA. It is also found that VTRA1.1 had reduced interaction of RecA with LexA and ssDNA polydT, showing the lead's efficacy in controlling the SOS response. Further, it was also observed that VTRA1.1 does not contain any predicted human off-targets and no cytotoxicity to cell lines. As functional RecA is involved in antimicrobial resistance, denovo designed lead VTRA1.1 against RecA may be further developed as a significant combination for therapeutic uses against A. baumannii.
    MeSH term(s) Acinetobacter baumannii/metabolism ; Anti-Bacterial Agents/metabolism ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism ; DNA Repair ; Humans ; Molecular Dynamics Simulation ; Rec A Recombinases/chemistry ; Rec A Recombinases/genetics ; Rec A Recombinases/metabolism
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Rec A Recombinases (EC 2.7.7.-)
    Language English
    Publishing date 2022-03-29
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2216600-2
    ISSN 1747-0285 ; 1747-0277
    ISSN (online) 1747-0285
    ISSN 1747-0277
    DOI 10.1111/cbdd.14037
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Denovo designing, retro-combinatorial synthesis, and molecular dynamics analysis identify novel antiviral VTRM1.1 against RNA-dependent RNA polymerase of SARS CoV2 virus.

    Tiwari, Vishvanath

    International journal of biological macromolecules

    2021  Volume 171, Page(s) 358–365

    Abstract: A novel coronavirus disease (COVID-19) caused by SARS-CoV2 has now spread globally. Replication/transcription machinery of this virus consists of RNA-dependent RNA polymerase (nsp12 or RdRp) and its two cofactors nsp7 and nsp8 proteins. Hence, RdRp has ... ...

    Abstract A novel coronavirus disease (COVID-19) caused by SARS-CoV2 has now spread globally. Replication/transcription machinery of this virus consists of RNA-dependent RNA polymerase (nsp12 or RdRp) and its two cofactors nsp7 and nsp8 proteins. Hence, RdRp has emerged as a promising target to control COVID-19. In the present study, we are reporting a novel inhibitor VTRM1.1 against the RdRp protein of SARS CoV2. A series of antivirals were tested for binding to the catalytic residues of the active site of RdRp protein. In-silico screening, molecular mechanics, molecular dynamics simulation (MDS) analysis suggest ribavirin, and remdesivir have good interaction with the binding site of the RdRp protein as compared to other antiviral investigated. Hence, ribavirin and remdesivir were used for the denovo fragments based antiviral design. This design, along with docking and MDS analysis, identified a novel inhibitor VTRM1 that has better interaction with RdRp as compared to their parent molecules. Further, to produce a lead-like compound, retrosynthetic analysis, and combinatorial synthesis were performed, which produces 1000 analogs of VTRM1. These analogs were analysed by docking and MDS analysis that identified VTRM1.1 as a possible lead to inhibit RdRp protein. This lead has a good docking score, favourable binding energy and bind at catalytic residues of the active site of RdRp. The VTRM1.1 also interacts with RdRp in the presence of RNA primer and other cofactors. It was also seen that, VTRM1.1 do not have off-target in human. Therefore, the present study suggests a hybrid inhibitor VTRM1.1 for the RNA-dependent RNA polymerase of SARS CoV2 that may be useful to control infection caused by COVID-19.
    Language English
    Publishing date 2021-01-07
    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.2020.12.223
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Assessment of potassium ion channel during electric signalling in biofilm formation of

    Tiwari, Monalisa / Panwar, Shruti / Tiwari, Vishvanath

    Heliyon

    2023  Volume 9, Issue 1, Page(s) e12837

    Abstract: Acinetobacter ... ...

    Abstract Acinetobacter baumannii
    Language English
    Publishing date 2023-01-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2023.e12837
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Novel hybrid antiviral VTRRT-13V2.1 against SARS-CoV2 main protease: retro-combinatorial synthesis and molecular dynamics analysis.

    Tiwari, Vishvanath

    Heliyon

    2020  Volume 6, Issue 10, Page(s) e05122

    Abstract: The COVID-19 pandemic caused by SARS-CoV-2 has now emerged as a global health problem and is responsible for high mortality and morbidity. The SARS-CoV-2 main protease ( ... ...

    Abstract The COVID-19 pandemic caused by SARS-CoV-2 has now emerged as a global health problem and is responsible for high mortality and morbidity. The SARS-CoV-2 main protease (M
    Keywords covid19
    Language English
    Publishing date 2020-09-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e05122
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: De novo

    Tiwari, Vishvanath

    Biology open

    2020  Volume 9, Issue 10

    Abstract: SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin ... ...

    Abstract SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a
    MeSH term(s) Angiotensin-Converting Enzyme 2 ; Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Betacoronavirus/metabolism ; Cell Death/drug effects ; Combinatorial Chemistry Techniques ; Humans ; Molecular Docking Simulation ; Peptidyl-Dipeptidase A/chemistry ; Peptidyl-Dipeptidase A/metabolism ; Protein Binding/drug effects ; Protein Domains ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/metabolism ; Thermodynamics
    Chemical Substances Antiviral Agents ; Spike Glycoprotein, Coronavirus ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Keywords covid19
    Language English
    Publishing date 2020-10-15
    Publishing country England
    Document type Journal Article
    ZDB-ID 2632264-X
    ISSN 2046-6390 ; 2046-6390
    ISSN (online) 2046-6390
    ISSN 2046-6390
    DOI 10.1242/bio.054056
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: De novo design, retrosynthetic analysis and combinatorial synthesis of a hybrid antiviral (VTAR-01) to inhibit the interaction of SARS-CoV2 spike glycoprotein with human angiotensin-converting enzyme 2

    Vishvanath Tiwari

    Biology Open, Vol 9, Iss

    2020  Volume 10

    Abstract: SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin ... ...

    Abstract SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a de novo designed novel hybrid antiviral ‘VTAR-01’ molecule that binds at the interface of RBD-hACE2 interaction. A series of antiviral molecules were tested for binding at the interface of RBD-hACE2 interaction. In silico screening, molecular mechanics and molecular dynamics simulation (MDS) analysis suggest ribavirin, ascorbate, lopinavir and hydroxychloroquine have strong interaction at the RBD-hACE2 interface. These four molecules were used for de novo fragment-based antiviral design. De novo designing, docking and MDS analysis identified a ‘VTAR’ hybrid molecule that has better interaction with this interface than all of the antivirals used to design it. We have further used retrosynthetic analysis and combinatorial synthesis to design 100 variants of VTAR molecules. Retrosynthetic analysis and combinatorial synthesis, along with docking and MDS, identified that VTAR-01 interacts with the interface of the RBD-ACE2 complex. MDS analysis confirmed its interaction with the RBD-ACE2 interface by involving Glu35 and Lys353 of ACE2, as well as Gln493 and Ser494 of RBD. Interaction of spike protein with ACE2 is essential for pathogenesis and infection of this virus; hence, this in silico designed hybrid antiviral molecule (VTAR-01) that binds at the interface of RBD-hACE2 may be further developed to control the infection of SARS-CoV2.
    Keywords hybrid antiviral molecule ; sars-cov2 spike glycoprotein ; angiotensin converting enzyme 2 ; de novo designing ; retrosynthetic analysis ; molecular dynamics simulation ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 572
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher The Company of Biologists
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Novel hybrid antiviral VTRRT-13V2.1 against SARS-CoV2 main protease

    Vishvanath Tiwari

    Heliyon, Vol 6, Iss 10, Pp e05122- (2020)

    retro-combinatorial synthesis and molecular dynamics analysis

    2020  

    Abstract: The COVID-19 pandemic caused by SARS-CoV-2 has now emerged as a global health problem and is responsible for high mortality and morbidity. The SARS-CoV-2 main protease (Mpro) emerged as a promising drug target because of its essential role in the ... ...

    Abstract The COVID-19 pandemic caused by SARS-CoV-2 has now emerged as a global health problem and is responsible for high mortality and morbidity. The SARS-CoV-2 main protease (Mpro) emerged as a promising drug target because of its essential role in the processing of polyproteins, which is translated from viral RNA. The present study reports a designed novel hybrid antiviral molecule (VTRRT-13.V2.1) against SARS-CoV2 main protease. A series of different combinations of hybrid antiviral were generated from nonspecific antiviral molecules currently used to control COVID-19. To enhance the specificity of the designed hybrid antiviral molecule, the core pocket region of the active site of Mpro protein was targeted. In-silico screening, molecular mechanics, molecular dynamics simulation (MDS) analysis identified a hybrid VTRRT-13.V2 molecule. Retrosynthetic analysis and combinatorial synthesis generated 1000 analogs of VTRRT-13.V2 molecules. Docking, molecular mechanics, and MDS analysis selected VTRRT-13.V2.1 as a possible inhibitor for SARS-CoV2 main protease. Comparative analysis of all the results showed that VTRRT-13.V2.1 have the highest docking Glide score (-12.28 kcal/mol) and best binding energy (-52.23 kcal/mol) as compared to the other hybrid constructs such as VTRRT-13.V2 (-9.47 and -47.36 kcal/mol), VTRRT-13 (-8.9 and -47.55 kcal/mol), and current antiviral investigated. The mutational sensitivity screening showed that binding residues of Mpro are not present in mutation hotspots. It was also observed that VTRRT-13.V2.1 does not have any human off-targets. SARS-CoV2 main protease is essential for the survival of this virus; hence, a designed novel hybrid antiviral molecule (VTRRT-13.V2.1) might be useful to control the infection of COVID-19 infection.
    Keywords Bioinformatics ; Microbiology ; Infectious disease ; Medical microbiology ; Hybrid antiviral molecule ; SARS-CoV2 main protease ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99 ; covid19
    Subject code 541
    Language English
    Publishing date 2020-10-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Interaction and simulation studies suggest the possible molecular targets of intrinsically disordered amyloidogenic antimicrobial peptides in

    Sarkar, Sayani / Kumari, Aruna / Tiwari, Monalisa / Tiwari, Vishvanath

    Journal of biomolecular structure & dynamics

    2023  Volume 42, Issue 6, Page(s) 2747–2764

    Abstract: Acinetobacter ... ...

    Abstract Acinetobacter baumannii
    MeSH term(s) Antimicrobial Peptides ; Acinetobacter baumannii ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/chemistry ; Microbial Sensitivity Tests
    Chemical Substances Antimicrobial Peptides ; Anti-Bacterial Agents
    Language English
    Publishing date 2023-05-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2208219
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  10. Article ; Online: Novel hybrid antiviral VTRRT-13V2.1 against SARS-CoV2 main protease

    Tiwari, Vishvanath

    Heliyon

    retro-combinatorial synthesis and molecular dynamics analysis

    2020  Volume 6, Issue 10, Page(s) e05122

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    ZDB-ID 2835763-2
    ISSN 2405-8440
    ISSN 2405-8440
    DOI 10.1016/j.heliyon.2020.e05122
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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