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  1. Article ; Online: Thalidomide interaction with inflammation in idiopathic pulmonary fibrosis.

    Dsouza, Nikitha Naomi / Alampady, Varun / Baby, Krishnaprasad / Maity, Swastika / Byregowda, Bharath Harohalli / Nayak, Yogendra

    Inflammopharmacology

    2023  Volume 31, Issue 3, Page(s) 1167–1182

    Abstract: The "Thalidomide tragedy" is a landmark in the history of the pharmaceutical industry. Despite limited clinical trials, there is a continuous effort to investigate thalidomide as a drug for cancer and inflammatory diseases such as rheumatoid arthritis, ... ...

    Abstract The "Thalidomide tragedy" is a landmark in the history of the pharmaceutical industry. Despite limited clinical trials, there is a continuous effort to investigate thalidomide as a drug for cancer and inflammatory diseases such as rheumatoid arthritis, lepromatous leprosy, and COVID-19. This review focuses on the possibilities of targeting inflammation by repurposing thalidomide for the treatment of idiopathic pulmonary fibrosis (IPF). Articles were searched from the Scopus database, sorted, and selected articles were reviewed. The content includes the proven mechanisms of action of thalidomide relevant to IPF. Inflammation, oxidative stress, and epigenetic mechanisms are major pathogenic factors in IPF. Transforming growth factor-β (TGF-β) is the major biomarker of IPF. Thalidomide is an effective anti-inflammatory drug in inhibiting TGF-β, interleukins (IL-6 and IL-1β), and tumour necrosis factor-α (TNF-α). Thalidomide binds cereblon, a process that is involved in the proposed mechanism in specific cancers such as breast cancer, colon cancer, multiple myeloma, and lung cancer. Cereblon is involved in activating AMP-activated protein kinase (AMPK)-TGF-β/Smad signalling, thereby attenuating fibrosis. The past few years have witnessed an improvement in the identification of biomarkers and diagnostic technologies in respiratory diseases, partly because of the COVID-19 pandemic. Hence, investment in clinical trials with a systematic plan can help repurpose thalidomide for pulmonary fibrosis.
    MeSH term(s) Humans ; Idiopathic Pulmonary Fibrosis/drug therapy ; Idiopathic Pulmonary Fibrosis/metabolism ; Inflammation/drug therapy ; Inflammation/metabolism ; Lung/metabolism ; Thalidomide/therapeutic use ; Thalidomide/metabolism ; Thalidomide/pharmacology ; Transforming Growth Factor beta/metabolism ; Immunosuppressive Agents/pharmacokinetics ; Immunosuppressive Agents/pharmacology ; Immunosuppressive Agents/therapeutic use
    Chemical Substances Thalidomide (4Z8R6ORS6L) ; Transforming Growth Factor beta ; Immunosuppressive Agents
    Language English
    Publishing date 2023-03-25
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 1080058-x
    ISSN 1568-5608 ; 0925-4692
    ISSN (online) 1568-5608
    ISSN 0925-4692
    DOI 10.1007/s10787-023-01193-1
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 3274: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

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  2. Article ; Online: Computational drug repurposing of Akt-1 allosteric inhibitors for non-small cell lung cancer.

    Baby, Krishnaprasad / Maity, Swastika / Mehta, Chetan Hasmukh / Nayak, Usha Y / Shenoy, Gautham G / Pai, Karkala Sreedhara Ranganath / Harikumar, Kuzhuvelil B / Nayak, Yogendra

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 7947

    Abstract: Non-small cell lung carcinomas (NSCLC) are the predominant form of lung malignancy and the reason for the highest number of cancer-related deaths. Widespread deregulation of Akt, a serine/threonine kinase, has been reported in NSCLC. Allosteric Akt ... ...

    Abstract Non-small cell lung carcinomas (NSCLC) are the predominant form of lung malignancy and the reason for the highest number of cancer-related deaths. Widespread deregulation of Akt, a serine/threonine kinase, has been reported in NSCLC. Allosteric Akt inhibitors bind in the space separating the Pleckstrin homology (PH) and catalytic domains, typically with tryptophan residue (Trp-80). This could decrease the regulatory site phosphorylation by stabilizing the PH-in conformation. Hence, in this study, a computational investigation was undertaken to identify allosteric Akt-1 inhibitors from FDA-approved drugs. The molecules were docked at standard precision (SP) and extra-precision (XP), followed by Prime molecular mechanics-generalized Born surface area (MM-GBSA), and molecular dynamics (MD) simulations on selected hits. Post XP-docking, fourteen best hits were identified from a library of 2115 optimized FDA-approved compounds, demonstrating several beneficial interactions such as pi-pi stacking, pi-cation, direct, and water-bridged hydrogen bonds with the crucial residues (Trp-80 and Tyr-272) and several amino acid residues in the allosteric ligand-binding pocket of Akt-1. Subsequent MD simulations to verify the stability of chosen drugs to the Akt-1 allosteric site showed valganciclovir, dasatinib, indacaterol, and novobiocin to have high stability. Further, predictions for possible biological interactions were performed using computational tools such as ProTox-II, CLC-Pred, and PASSOnline. The shortlisted drugs open a new class of allosteric Akt-1 inhibitors for the therapy of NSCLC.
    MeSH term(s) Humans ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Proto-Oncogene Proteins c-akt/metabolism ; Drug Repositioning ; Molecular Docking Simulation ; Lung Neoplasms/drug therapy ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/chemistry ; Molecular Dynamics Simulation
    Chemical Substances Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Protein Kinase Inhibitors
    Language English
    Publishing date 2023-05-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-35122-7
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  3. Article ; Online: SARS-CoV-2 entry inhibitors by dual targeting TMPRSS2 and ACE2: An in silico drug repurposing study.

    Baby, Krishnaprasad / Maity, Swastika / Mehta, Chetan H / Suresh, Akhil / Nayak, Usha Y / Nayak, Yogendra

    European journal of pharmacology

    2021  Volume 896, Page(s) 173922

    Abstract: The coronavirus disease (COVID-19) is spreading between human populations mainly through nasal droplets. Currently, the vaccines have great hope, but it takes years for testing its efficacy in human. As there is no specific drug treatment available for ... ...

    Abstract The coronavirus disease (COVID-19) is spreading between human populations mainly through nasal droplets. Currently, the vaccines have great hope, but it takes years for testing its efficacy in human. As there is no specific drug treatment available for COVID-19 pandemic, we explored in silico repurposing of drugs with dual inhibition properties by targeting transmembrane serine protease 2 (TMPRSS2) and human angiotensin-converting enzyme 2 (ACE2) from FDA-approved drugs. The TMPRSS2 and ACE2 dual inhibitors in COVID-19 would be a novel antiviral class of drugs called "entry inhibitors." For this purpose, approximately 2800 US-FDA approved drugs were docked using a virtual docking tool with the targets TMPRSS2 and ACE2. The best-fit drugs were selected as per docking scores and visual outcomes. Later on, drugs were selected on the basis of molecular dynamics simulations. The drugs alvimopan, arbekacin, dequalinum, fleroxacin, lopinavir, and valrubicin were shortlisted by visual analysis and molecular dynamics simulations. Among these, lopinavir and valrubicin were found to be superior in terms of dual inhibition. Thus, lopinavir and valrubicin have the potential of dual-target inhibition whereby preventing SARS-CoV-2 entry to the host. For repurposing of these drugs, further screening in vitro and in vivo would help in exploring clinically.
    MeSH term(s) Angiotensin-Converting Enzyme 2/antagonists & inhibitors ; Antiviral Agents/pharmacology ; COVID-19/drug therapy ; COVID-19/metabolism ; Doxorubicin/analogs & derivatives ; Doxorubicin/pharmacology ; Drug Repositioning ; Enzyme Inhibitors/classification ; Enzyme Inhibitors/pharmacology ; Humans ; Lopinavir/pharmacology ; Molecular Docking Simulation/methods ; Molecular Dynamics Simulation ; SARS-CoV-2/drug effects ; SARS-CoV-2/physiology ; Serine Endopeptidases/metabolism ; Topoisomerase II Inhibitors/pharmacology ; Virus Internalization/drug effects
    Chemical Substances Antiviral Agents ; Enzyme Inhibitors ; Topoisomerase II Inhibitors ; Lopinavir (2494G1JF75) ; valrubicin (2C6NUM6878) ; Doxorubicin (80168379AG) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Serine Endopeptidases (EC 3.4.21.-) ; TMPRSS2 protein, human (EC 3.4.21.-)
    Language English
    Publishing date 2021-02-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 80121-5
    ISSN 1879-0712 ; 0014-2999
    ISSN (online) 1879-0712
    ISSN 0014-2999
    DOI 10.1016/j.ejphar.2021.173922
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 522: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: Targeting SARS-CoV-2 RNA-dependent RNA polymerase: An

    Baby, Krishnaprasad / Maity, Swastika / Mehta, Chetan H / Suresh, Akhil / Nayak, Usha Y / Nayak, Yogendra

    F1000Research

    2020  Volume 9, Page(s) 1166

    Abstract: Background: ...

    Abstract Background:
    MeSH term(s) Antiviral Agents/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/enzymology ; COVID-19 ; Catalytic Domain ; Coronavirus Infections/drug therapy ; Drug Repositioning ; Humans ; Molecular Docking Simulation ; Pandemics ; Pentanoic Acids/pharmacology ; Pneumonia, Viral/drug therapy ; Pyridines/pharmacology ; Quinolines/pharmacology ; Quinolones/pharmacology ; RNA-Dependent RNA Polymerase/antagonists & inhibitors ; SARS-CoV-2 ; COVID-19 Drug Treatment
    Chemical Substances Antiviral Agents ; Pentanoic Acids ; Pyridines ; Quinolines ; Quinolones ; rosoxacin (3Y1OT3J4NW) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; pitavastatin (M5681Q5F9P) ; ridogrel (QTS5QOO42O)
    Keywords covid19
    Language English
    Publishing date 2020-09-23
    Publishing country England
    Document type Journal Article
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.26359.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Targeting SARS-CoV-2 Main Protease: A Computational Drug Repurposing Study.

    Baby, Krishnaprasad / Maity, Swastika / Mehta, Chetan H / Suresh, Akhil / Nayak, Usha Y / Nayak, Yogendra

    Archives of medical research

    2020  Volume 52, Issue 1, Page(s) 38–47

    Abstract: Background and aims: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) induced Novel Coronavirus Disease (COVID-19) has currently become pandemic worldwide. Though drugs like remdesivir, favipiravir, and dexamethasone found beneficial for ... ...

    Abstract Background and aims: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) induced Novel Coronavirus Disease (COVID-19) has currently become pandemic worldwide. Though drugs like remdesivir, favipiravir, and dexamethasone found beneficial for COVID-19 management, they have limitations clinically, and vaccine development takes a long time. The researchers have reported key proteins which could act as druggable targets. Among them, the major protease M
    Methods: The protein M
    Results: The docking and molecular interactions studies, five drugs emerged as potential hits by forming hydrophilic, hydrophobic, electrostatic interactions. The drugs such as arbutin, terbutaline, barnidipine, tipiracil and aprepitant identified as potential hits. Among the drugs, tipiracil and aprepitant interacted with the M
    Conclusions: This study shows the possible exploration for drug repurposing using computer-aided docking tools and the potential roles of tipiracil and aprepitant, which can be explored further in the treatment of COVID-19.
    MeSH term(s) Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; COVID-19/virology ; Coronavirus 3C Proteases/antagonists & inhibitors ; Coronavirus 3C Proteases/chemistry ; Coronavirus 3C Proteases/metabolism ; Drug Discovery/methods ; Drug Repositioning/methods ; Humans ; Molecular Docking Simulation/methods ; Molecular Dynamics Simulation ; Molecular Targeted Therapy ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; Protease Inhibitors/therapeutic use ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; COVID-19 Drug Treatment
    Chemical Substances Antiviral Agents ; Protease Inhibitors ; 3C-like protease, SARS coronavirus (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Keywords covid19
    Language English
    Publishing date 2020-09-17
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1156844-6
    ISSN 1873-5487 ; 0188-4409 ; 0188-0128
    ISSN (online) 1873-5487
    ISSN 0188-4409 ; 0188-0128
    DOI 10.1016/j.arcmed.2020.09.013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 1001: 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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  6. Article ; Online: Targeting SARS-CoV-2 RNA-dependent RNA polymerase

    Krishnaprasad Baby / Swastika Maity / Chetan H. Mehta / Akhil Suresh / Usha Y. Nayak / Yogendra Nayak

    F1000Research, Vol

    An in silico drug repurposing for COVID-19 [version 1; peer review: 2 approved]

    2020  Volume 9

    Abstract: Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), took more lives than combined epidemics of SARS, MERS, H1N1, and Ebola. Currently, the prevention and control of spread ... ...

    Abstract Background: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), took more lives than combined epidemics of SARS, MERS, H1N1, and Ebola. Currently, the prevention and control of spread are the goals in COVID-19 management as there are no specific drugs to cure or vaccines available for prevention. Hence, the drug repurposing was explored by many research groups, and many target proteins have been examined. The major protease (Mpro), and RNA-dependent RNA polymerase (RdRp) are two target proteins in SARS-CoV-2 that have been validated and extensively studied for drug development in COVID-19. The RdRp shares a high degree of homology between those of two previously known coronaviruses, SARS-CoV and MERS-CoV. Methods: In this study, the FDA approved library of drugs were docked against the active site of RdRp using Schrodinger's computer-aided drug discovery tools for in silico drug-repurposing. Results: We have shortlisted 14 drugs from the Standard Precision docking and interaction-wise study of drug-binding with the active site on the enzyme. These drugs are antibiotics, NSAIDs, hypolipidemic, coagulant, thrombolytic, and anti-allergics. In molecular dynamics simulations, pitavastatin, ridogrel and rosoxacin displayed superior binding with the active site through ARG555 and divalent magnesium. Conclusion: Pitavastatin, ridogrel and rosoxacin can be further optimized in preclinical and clinical studies to determine their possible role in COVID-19 treatment.
    Keywords Medicine ; R ; Science ; Q
    Subject code 572
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Targeting SARS-CoV-2 Main Protease

    Baby, Krishnaprasad / Maity, Swastika / Mehta, Chetan H. / Suresh, Akhil / Nayak, Usha Y. / Nayak, Yogendra

    Archives of Medical Research ; ISSN 0188-4409

    A Computational Drug Repurposing Study

    2020  

    Keywords General Medicine ; covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    DOI 10.1016/j.arcmed.2020.09.013
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Targeting SARS-CoV-2 Main Protease: A Computational Drug Repurposing Study

    Baby, Krishnaprasad / Maity, Swastika / Mehta, Chetan H / Suresh, Akhil / Nayak, Usha Y / Nayak, Yogendra

    Arch. med. res

    Abstract: BACKGROUND AND AIMS: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) induced Novel Coronavirus Disease (COVID-19) has currently become pandemic worldwide. Though drugs like remdesivir, favipiravir, and dexamethasone found beneficial for ... ...

    Abstract BACKGROUND AND AIMS: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) induced Novel Coronavirus Disease (COVID-19) has currently become pandemic worldwide. Though drugs like remdesivir, favipiravir, and dexamethasone found beneficial for COVID-19 management, they have limitations clinically, and vaccine development takes a long time. The researchers have reported key proteins which could act as druggable targets. Among them, the major protease Mpro is first published, plays a prominent role in viral replication and an attractive drug-target for drug discovery. Hence, to target Mpro and inhibit it, we accomplished the virtual screening of US-FDA approved drugs using well-known drug repurposing approach by computer-aided tools. METHODS: The protein Mpro, PDB-ID 6LU7 was imported to Maestro graphical user interphase of Schrödinger software. The US-FDA approved drug structures are imported from DrugBank and docked after preliminary protein and ligand preparation. The drugs are shortlisted based on the docking scores in the Standard Precision method (SP-docking) and then based on the type of molecular interactions they are studied for molecular dynamics simulations. RESULTS: The docking and molecular interactions studies, five drugs emerged as potential hits by forming hydrophilic, hydrophobic, electrostatic interactions. The drugs such as arbutin, terbutaline, barnidipine, tipiracil and aprepitant identified as potential hits. Among the drugs, tipiracil and aprepitant interacted with the Mpro consistently, and they turned out to be most promising. CONCLUSIONS: This study shows the possible exploration for drug repurposing using computer-aided docking tools and the potential roles of tipiracil and aprepitant, which can be explored further in the treatment of COVID-19.
    Keywords covid19
    Publisher WHO
    Document type Article
    Note WHO #Covidence: #773866
    Database COVID19

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