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  1. Article ; Online: Probing the inhibition of MAO-B by chalcones: an integrated approach combining molecular docking, ADME analysis, MD simulation, and MM-PBSA calculations.

    Jose, Jisna / Varughese, Jibin K / Parvez, Mohammad Khalid / Mathew, Thomas V

    Journal of molecular modeling

    2024  Volume 30, Issue 4, Page(s) 103

    Abstract: Context: Monoamine oxidase B (MAO-B), an enzyme of significant relevance in the realm of neurodegenerative disorders, has garnered considerable attention as a potential target for therapeutic intervention. Natural compounds known as chalcones have shown ...

    Abstract Context: Monoamine oxidase B (MAO-B), an enzyme of significant relevance in the realm of neurodegenerative disorders, has garnered considerable attention as a potential target for therapeutic intervention. Natural compounds known as chalcones have shown potential as MAO-B inhibitors. In this particular study, we employed a multimodal computational method to evaluate the inhibitory effects of chalcones on MAO-B.
    Methods: Molecular docking methods were used to study and assess the complicated binding interactions that occur between chalcones and MAO-B. This extensive analysis provided a valuable and deep understanding of possible binding methods as well as the key residues implicated in the inhibition process. Furthermore, the ADME investigation gave valuable insights into the pharmacokinetic properties of chalcones. This allowed them to be assessed in terms of drug-like attributes. The use of MD simulations has benefited in the research of ligand-protein interactions' dynamic behaviour and temporal stability. MM-PBSA calculations were also done to estimate the binding free energies and acquire a better knowledge and understanding of the binding affinity between chalcones and MAO-B. Our thorough method gives a thorough knowledge of chalcones' potential as MAO-B inhibitors, which will be useful for future experimental validation and drug development efforts in the context of neurodegenerative illnesses.
    MeSH term(s) Monoamine Oxidase/chemistry ; Monoamine Oxidase/metabolism ; Molecular Docking Simulation ; Monoamine Oxidase Inhibitors/pharmacology ; Monoamine Oxidase Inhibitors/chemistry ; Chalcones/pharmacology ; Chalcones/chemistry ; Structure-Activity Relationship
    Chemical Substances Monoamine Oxidase (EC 1.4.3.4) ; Monoamine Oxidase Inhibitors ; Chalcones
    Language English
    Publishing date 2024-03-13
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1284729-X
    ISSN 0948-5023 ; 1610-2940
    ISSN (online) 0948-5023
    ISSN 1610-2940
    DOI 10.1007/s00894-024-05889-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Biomolecular interactions between the antibacterial ceftolozane and the human inflammatory disease target ADAM17: a drug repurposing study.

    Sunil, Ahsan Anjoom / Jose, Deepthi / Karri, Sai Kumar / Pukhraj, Pukhraj / Varughese, Jibin K / Skaria, Tom

    Journal of biomolecular structure & dynamics

    2023  , Page(s) 1–11

    Abstract: Inhibition of a disintegrin and metalloproteinase-17 (ADAM17), a metzincin, is proposed as a novel therapeutic strategy to suppress overproduction of the proinflammatory cytokine TNF-α in rheumatoid arthritis and inflammatory bowel disease. Existing ... ...

    Abstract Inhibition of a disintegrin and metalloproteinase-17 (ADAM17), a metzincin, is proposed as a novel therapeutic strategy to suppress overproduction of the proinflammatory cytokine TNF-α in rheumatoid arthritis and inflammatory bowel disease. Existing ADAM17 inhibitors generate toxic metabolites
    Language English
    Publishing date 2023-10-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2263895
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Investigation of the inhibitory activity of some dietary bioactive flavonoids against SARS-CoV-2 using molecular dynamics simulations and MM-PBSA calculations.

    Varughese, Jibin K / Joseph Libin, K L / Sindhu, K S / Rosily, A V / Abi, T G

    Journal of biomolecular structure & dynamics

    2021  Volume 40, Issue 15, Page(s) 6755–6770

    Abstract: Eventhough the development of vaccine against COVID-19 pandemic is progressing in different part of the world a well-defined treatment plan is not yet developed. Therefore, we investigate the inhibitory activity of a group of dietary bioactive flavonoids ...

    Abstract Eventhough the development of vaccine against COVID-19 pandemic is progressing in different part of the world a well-defined treatment plan is not yet developed. Therefore, we investigate the inhibitory activity of a group of dietary bioactive flavonoids against SARS-CoV-2 main protease (M
    MeSH term(s) Humans ; COVID-19/prevention & control ; COVID-19 Drug Treatment ; COVID-19 Vaccines ; Cysteine Endopeptidases/chemistry ; Flavonoids/pharmacology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors/chemistry ; SARS-CoV-2
    Chemical Substances COVID-19 Vaccines ; Cysteine Endopeptidases (EC 3.4.22.-) ; Flavonoids ; Protease Inhibitors
    Language English
    Publishing date 2021-02-23
    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 10.1080/07391102.2021.1891139
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Identification of some dietary flavonoids as potential inhibitors of TMPRSS2 through protein-ligand interaction studies and binding free energy calculations.

    Varughese, Jibin K / J, Kavitha / S, Sindhu K / Francis, Dhiya / L, Joseph Libin K / G, Abi T

    Structural chemistry

    2022  Volume 33, Issue 5, Page(s) 1489–1502

    Abstract: The continuing threat of COVID-19 and deaths need an urgent cost-effective pharmacological approach. Here, we examine the inhibitory activity of a group of dietary bioactive flavonoids against the human protease TMPRSS2, which plays a major role in SARS ... ...

    Abstract The continuing threat of COVID-19 and deaths need an urgent cost-effective pharmacological approach. Here, we examine the inhibitory activity of a group of dietary bioactive flavonoids against the human protease TMPRSS2, which plays a major role in SARS CoV-2 viral entry. After the molecular docking studies of a large number of flavonoids, four compounds with high binding scores were selected and studied in detail. The binding affinities of these four ligands, Amentoflavone, Narirutin, Eriocitrin, and Naringin, at the active site of the TMPRSS2 target, were investigated using MD simulations followed by MM-PBSA binding energy calculations. From the studies, a number of significant hydrophobic and hydrogen bonding interactions between the ligands and binding site amino residues of TMPRSS2 are identified which showcase their excellent inhibitory activity against TMPRSS2. Among these ligands, Amentoflavone and Narirutin showed MM-PBSA binding energy values of -155.57 and -139.71 kJ/mol, respectively. Our previous studies of the inhibitory activity of these compounds against the main protease of SARS-COV2 and the present study on TMPRSS2 strongly highlighted that Amentoflavone and Naringin can exhibit promising multi-target activity against SARS-CoV-2. Moreover, due to their wide availability, no side effects, and low cost, these compounds could be recommended as dietary supplements for COVID patients or for the development of SARS-CoV-2 treatments.
    Supplementary information: The online version contains supplementary material available at 10.1007/s11224-022-01955-7.
    Language English
    Publishing date 2022-05-25
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2018832-8
    ISSN 1572-9001 ; 1040-0400
    ISSN (online) 1572-9001
    ISSN 1040-0400
    DOI 10.1007/s11224-022-01955-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Targeting COVID-19 pandemic: in silico evaluation of 2-hydroxy-1, 2-diphenylethanone N(4)-methyl-N(4)-phenylthiosemicarbazone as a potential inhibitor of SARS-CoV-2.

    Jeevana, Rajan / Kavitha, Abu Pilakkaveettil / Abi, Thoppilan G / Sajith, Pookkottu K / Varughese, Jibin K / Aravindakshan, Kuttamath Kunniyur

    Structural chemistry

    2022  , Page(s) 1–17

    Abstract: The global spread of the COVID-19 pandemic caused by the etiological agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), triggered researchers to identify and develop novel antiviral therapeutics. Herein, we report a new molecule 2- ... ...

    Abstract The global spread of the COVID-19 pandemic caused by the etiological agent, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), triggered researchers to identify and develop novel antiviral therapeutics. Herein, we report a new molecule 2-hydroxy-1,2-diphenylethanone N(4)-methyl-N(4)-phenyl thiosemicarbazone (BMPTSC), as a potential inhibitor of SARS-CoV-2. BMPTSC was synthesized, characterized by IR and NMR studies, and the structural parameters were analyzed computationally by B3LYP/cc-pVDZ method. Molecular docking studies were performed to get insights into the energetics and compatibility of BMPTSC against various SARS-CoV-2 drug targets. The best docking poses of target protein-BMPTSC complex structures were further subjected to molecular dynamics (MD) simulations. Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations on the binding of BMPTSC with the target proteins viz. spike glycoprotein and ACE-2 protein showed energy values of -179.87 and -145.61 kJ/mol, respectively. Moreover, BMPTSC obeys Lipinski's rule, and further in silico assessment of oral bioavailability, bioactivity scores, ADME, drug-likeness, and medicinal chemistry friendliness suggests that this molecule is a promising candidate for the COVID-19 drug discovery process.
    Supplementary information: The online version contains supplementary material available at 10.1007/s11224-022-02033-8.
    Language English
    Publishing date 2022-10-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2018832-8
    ISSN 1572-9001 ; 1040-0400
    ISSN (online) 1572-9001
    ISSN 1040-0400
    DOI 10.1007/s11224-022-02033-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Awareness of treatment options for dengue fever among the patients and their relatives attending a tertiary care hospital in central Kerala

    Jency Maria Koshy / Alice David / S K Mathew / Mohan Varughese / Sony Punnen Thomas / Jibin John Thomas

    Journal of Current Research in Scientific Medicine, Vol 4, Iss 1, Pp 30-

    2018  Volume 36

    Abstract: Introduction: Dengue virus infection is a major cause of morbidity, mortality, and economic hardship in the tropics and subtropics. We undertook this study to see the level of awareness of symptoms and the treatment options for dengue fever. Materials ... ...

    Abstract Introduction: Dengue virus infection is a major cause of morbidity, mortality, and economic hardship in the tropics and subtropics. We undertook this study to see the level of awareness of symptoms and the treatment options for dengue fever. Materials and Methods: This was a cross-sectional study done in the Department of Medicine at a tertiary medical care in central Kerala during July 2017. The patients and their attendants visiting outpatient department were interviewed by trained social workers after taking a written consent. The interview was conducted based on a structured questionnaire. Distribution of various aspects of awareness and sociodemographic characteristics are presented. The association of the awareness of treatment options with sociodemographic characteristics was estimated. Results: Among the 522 subjects interviewed 509 (97.51%) had heard about dengue. Majority of them (89.59%) were aware that this is a preventable disease. Newspaper (80.94%) and television (74.85%) were the main sources of information. Most (85.85%) of them were aware of the infectious nature of the disease and that mosquitoes are the responsible vector. The most common symptoms of this disease which they were aware of were fever (64.83%), body ache (62.48%) and headache (50.68%). Almost half (48.13%) of them incorrectly expressed the need for antibiotics for this viral illness and 46.37% felt the need for platelet transfusion to hasten the recovery. Only education was associated with better awareness regarding antibiotic use (odds ratio [OR] [95% confidence interval [CI]: 1.55 [1.03–2.34]) and platelet transfusion (OR [95% CI]: 2.40 [1.17–4.91]). Conclusions: They had a reasonably good awareness of the vector that promotes dengue and its breeding sites. However, there were misconceptions regarding the treatment options.
    Keywords Awareness ; dengue fever ; prevention ; Medicine ; R
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Wolters Kluwer Medknow Publications
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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