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Article ; Online: Mushrooms are potential foods against cancer: identified by molecular docking and molecular dynamics simulation.

Debnath, Sudhan / Sen, Debanjan

2021 Volume 36, Issue 10, Page(s) 2604–2609

Abstract: Epidermal Growth Factor Receptor (EGFR) is a promising drug target for the discovery of cancer chemotherapeutics. EGFR tyrosine kinase inhibitors become resistant due to mutation after a certain period of clinical application. The objective of the ... ...

Abstract	Epidermal Growth Factor Receptor (EGFR) is a promising drug target for the discovery of cancer chemotherapeutics. EGFR tyrosine kinase inhibitors become resistant due to mutation after a certain period of clinical application. The objective of the present study is to identify edible mushrooms as EGFR inhibitors. Structure-based VS of mushroom compounds using Autodock Vina in PyRx, re-docking of top scored hits using Autodock 4.2 were performed. Molecular dynamics (MD) was carried out with top hits to investigate the dynamic nature of the active site followed by MMPBSA binding energy calculation and ADME study. Analysis of MD results revealed the stability of Ag_76, Ag_77, Ag_88 and Ag_340 in the active site of EGFR as potential binders. Comparison of docking and MD results with known inhibitors also claimed the effectiveness of these hits. The sources of these potential hits are
MeSH term(s)	Agaricales/chemistry ; ErbB Receptors/metabolism ; Functional Food ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Neoplasms ; Protein Kinase Inhibitors/pharmacology
Chemical Substances	Protein Kinase Inhibitors ; ErbB Receptors (EC 2.7.10.1)
Language	English
Publishing date	2021-05-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2185747-7
ISSN	1478-6427 ; 1478-6419
ISSN (online)	1478-6427
ISSN	1478-6419
DOI	10.1080/14786419.2021.1912041
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Mushrooms are potential foods against cancer: identified by molecular docking and molecular dynamics simulation

Debnath, Sudhan / Sen, Debanjan

Natural product research. 2022 May 23, v. 36, no. 10

2022

Abstract	Epidermal Growth Factor Receptor (EGFR) is a promising drug target for the discovery of cancer chemotherapeutics. EGFR tyrosine kinase inhibitors become resistant due to mutation after a certain period of clinical application. The objective of the present study is to identify edible mushrooms as EGFR inhibitors. Structure-based VS of mushroom compounds using Autodock Vina in PyRx, re-docking of top scored hits using Autodock 4.2 were performed. Molecular dynamics (MD) was carried out with top hits to investigate the dynamic nature of the active site followed by MMPBSA binding energy calculation and ADME study. Analysis of MD results revealed the stability of Ag_76, Ag_77, Ag_88 and Ag_340 in the active site of EGFR as potential binders. Comparison of docking and MD results with known inhibitors also claimed the effectiveness of these hits. The sources of these potential hits are Polyozellus multiplex, Sarcodon imbricatus, and Cortinarius purpurascens, which may be effective as anti-cancer food after in vitro studies.
Keywords	Cortinarius ; Sarcodon ; active sites ; drug therapy ; drugs ; energy ; epidermal growth factor receptors ; molecular dynamics ; mushrooms ; mutation ; research ; tyrosine
Language	English
Dates of publication	2022-0523
Size	p. 2604-2609.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2185747-7
ISSN	1478-6427 ; 1478-6419
ISSN (online)	1478-6427
ISSN	1478-6419
DOI	10.1080/14786419.2021.1912041
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Potentiality of

Sen, Debanjan / Bhaumik, Samhita / Debnath, Pradip / Debnath, Sudhan

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 16, Page(s) 7517–7534

Abstract: Coronavirus disease 2019 (COVID-19) has created a global human health crisis and economic setbacks. Lack of specific therapeutics and limited treatment options against COVID-19 has become a new challenge to identify potential hits in order to develop new ...

Abstract	Coronavirus disease 2019 (COVID-19) has created a global human health crisis and economic setbacks. Lack of specific therapeutics and limited treatment options against COVID-19 has become a new challenge to identify potential hits in order to develop new therapeutics. One of the crucial life cycle enzymes of SARS-CoV-2 is main protease (M
MeSH term(s)	COVID-19/drug therapy ; Coronavirus 3C Proteases ; Cysteine Endopeptidases/chemistry ; Drug Design ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Moringa oleifera/metabolism ; Protease Inhibitors/chemistry ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry
Chemical Substances	Protease Inhibitors ; Viral Nonstructural Proteins ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2021-03-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1898475
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Article ; Online: Structure-based drug design-guided identification of estrogen receptor binders.

Samanta, Rojalini / Pradhan, Kishanta Kumar / Sen, Debanjan / Kar, Supratik / Ghosh, Manik

Molecular diversity

2023

Abstract: Cancer is one of the life-threatening diseases and the second leading cause of death in the world. The estrogen receptor can be considered as one of the significant drug targets for cancer. A large number of clinically used anticancer drugs were ... ...

Abstract	Cancer is one of the life-threatening diseases and the second leading cause of death in the world. The estrogen receptor can be considered as one of the significant drug targets for cancer. A large number of clinically used anticancer drugs were identified from phytochemicals. Multiple literatures suggested that extracts of Datura sp. significantly inhibit estrogen receptors associated with human cancer. In the present study, all reported natural products present in Datura sp. were subjected to molecular docking against estrogen receptors. The top hits were shortlisted based on binding orientation and docking score and subjected to molecular dynamics simulation to explore the conformational stability followed by binding energy calculation. The ligand [(1S,5R)-8-Methyl-8-Azabicyclo [3.2.1] Octan-3-yl] (2R)-3-Hydroxy-2-Phenylpropanoate depicts highly acceptable MD simulations outcomes and drug-likeness profile. Knowledge-based de novo design and similar ligand screening were executed using the structural information. The designed ligand DL-50 exhibited satisfactory binding, drug-likeness profile, and well-accepted ADMET profile followed by easy synthetic accessibility which further requires experimental validation.
Language	English
Publishing date	2023-06-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10657-z
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Zs.A 4946: Show issues

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Article ; Online: Phytochemicals of Zingiberaceae family exhibit potentiality against SARS-CoV-2 main protease identified by a rational computer-aided drug design.

Debnath, Sudhan / Bhaumik, Samhita / Sen, Debanjan / Debnath, Bimal

Natural product research

2021 Volume 36, Issue 17, Page(s) 4563–4568

Abstract: Coronavirus disease 2019 (COVID-19) has created huge social, economic and human health crises globally. Discovery of specific drugs has become a new challenge to the researcher. Structure-based virtual-screening of our in-house databank containing1102 ... ...

Abstract	Coronavirus disease 2019 (COVID-19) has created huge social, economic and human health crises globally. Discovery of specific drugs has become a new challenge to the researcher. Structure-based virtual-screening of our in-house databank containing1102 phytochemicals of Zingiberaceae family was performed with main protease(M
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/pharmacology ; COVID-19/drug therapy ; Coronavirus 3C Proteases ; Cysteine Endopeptidases ; Drug Design ; Humans ; Molecular Docking Simulation ; Phytochemicals/pharmacology ; Protease Inhibitors/chemistry ; Protease Inhibitors/pharmacology ; SARS-CoV-2 ; Viral Nonstructural Proteins ; Zingiberaceae/metabolism
Chemical Substances	Antiviral Agents ; Phytochemicals ; Protease Inhibitors ; Viral Nonstructural Proteins ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2021-10-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2185747-7
ISSN	1478-6427 ; 1478-6419
ISSN (online)	1478-6427
ISSN	1478-6419
DOI	10.1080/14786419.2021.1994563
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Article: Phytochemicals of Zingiberaceae family exhibit potentiality against SARS-CoV-2 main protease identified by a rational computer-aided drug design

Debnath, Sudhan / Bhaumik, Samhita / Sen, Debanjan / Debnath, Bimal

Natural product research. 2022 Sept. 1, v. 36, no. 17

2022

Abstract	Coronavirus disease 2019 (COVID-19) has created huge social, economic and human health crises globally. Discovery of specific drugs has become a new challenge to the researcher. Structure-based virtual-screening of our in-house databank containing1102 phytochemicals of Zingiberaceae family was performed with main protease(Mᵖʳᵒ), a crucial enzyme of SARS-CoV-2. Rigorous docking and ADME study of top-scored twenty hits resulted from VS was performed. Then 100 ns molecular dynamics followed by MMPBSA binding free energy(ΔGbᵢₙd) calculation of A280 and KZ133 was also performed. These two hits showed good interactions with crucial amino acid residues of Mᵖʳᵒ HIS-41 and CYS-145, excellent ADME properties, fair ΔGbᵢₙd values (> ‒188.03 kj/mol), and average protein-ligand complex RMSD < apo-protein RMSD. Therefore, the seed extracts of Alpinia blepharocalyx and rhizome extracts Kaempferia angustifolia containing A280 and KZ133, respectively, may be useful against COVID-19 after the proper biological screening. These two novel scaffolds could be exploited as potent SARS-CoV-2-Mᵖʳᵒ inhibitors.
Keywords	Alpinia ; Blepharocalyx ; COVID-19 infection ; Gibbs free energy ; Kaempferia angustifolia ; Severe acute respiratory syndrome coronavirus 2 ; amino acids ; databases ; drug design ; human health ; molecular dynamics ; phytochemicals ; proteinases ; research ; researchers ; rhizomes
Language	English
Dates of publication	2022-0901
Size	p. 4557-4562.
Publishing place	Taylor & Francis
Document type	Article
ZDB-ID	2185747-7
ISSN	1478-6427 ; 1478-6419
ISSN (online)	1478-6427
ISSN	1478-6419
DOI	10.1080/14786419.2021.1994563
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Article ; Online: Anti-inflammatory Potential of GSK-3 Inhibitors.

Kandar, Chandi C / Sen, Debanjan / Maity, Arindam

Current drug targets

2021 Volume 22, Issue 13, Page(s) 1464–1476

Abstract: Glycogen synthase kinase-3 (GSK-3) is a protein kinase containing threonine or serine amino acid residues. GSK-3 was first discovered in 1980 as a regulatory protein kinase, Glycogen synthase (GS) enzyme, which is responsible for the conversion of ... ...

Abstract	Glycogen synthase kinase-3 (GSK-3) is a protein kinase containing threonine or serine amino acid residues. GSK-3 was first discovered in 1980 as a regulatory protein kinase, Glycogen synthase (GS) enzyme, which is responsible for the conversion of glycogen from glucose with the help of uridine diphosphate glucose (UDP-Glu) residue. GSK-3 has two isoforms present in human beings, namely GSK-3 α (serine residue at 21 position) and GSK-3 β (serine residue at 9 position). GSK-3 has two terminals, namely C- terminal and N- terminal. C-terminal of GSK-3 resembles α- helix conformation, which acts as an activator loop and is responsible for positioning residues in ATP binding and catalysis of substrates. On the other hand, the N- terminal of GSK-3 resembles β- strand conformation, which acts as an inhibitory loop; having a tyrosine molecule at 216 positions, it is essential for the complete GSK-3 activity. N- terminal of GSK-3 is responsible for ATP binding activity and exhibits various biological activities like cell signaling, gene induction following activation of T cell receptor, apoptosis, protein translation, glycogen metabolism, and inflammatory process. Activation of GSK-3 leads to pro-inflammatory actions, i.e. an increase in the binding activity of NF-kB (pro-inflammatory genes), increase in the transactivation activity of NF-kB, increase in the phosphorylation of p105, and a decrease in the transactivation activity of C/EBPβ (anti- inflammatory genes), resulting in a large number of prevalent diseases such as diabetes, cancer, neurodegenerative diseases, psychiatric diseases, mood disorders, etc. Glycogen synthase kinase inhibitors (GSK-3 inhibitors) are various chemotypes and have different mechanisms of actions. They are obtained from different sources such as natural products, synthetic ATP as well as non-ATP competitive inhibitors along with substrate-competitive inhibitors. The inhibitors of GSK3 have proven to possess very potent anti-inflammatory action. GSK-3 inhibitors are useful for treating different prevalent disorders, such as neurodegenerative diseases, including Alzheimer's disease, hyperglycemia, cancer disease, and mood disorders like depression, etc. In this review, we have highlighted the evidence regarding the description and types of GSK, inflammation process, and the factors affecting inflammation, the relationship between inflammation and GSK, GSK3 inhibitors, and finally, the impact of various natural as well as synthetic GSK3 inhibitors having anti-inflammatory activity.
MeSH term(s)	Anti-Inflammatory Agents/therapeutic use ; Glycogen Synthase Kinase 3/antagonists & inhibitors ; Humans ; Inflammation/drug therapy ; Protein Kinase Inhibitors/therapeutic use
Chemical Substances	Anti-Inflammatory Agents ; Protein Kinase Inhibitors ; Glycogen Synthase Kinase 3 (EC 2.7.11.26)
Language	English
Publishing date	2021-01-08
Publishing country	United Arab Emirates
Document type	Journal Article ; Review
ZDB-ID	2064859-5
ISSN	1873-5592 ; 1389-4501
ISSN (online)	1873-5592
ISSN	1389-4501
DOI	10.2174/1389450122666210118150313
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Zs.A 5578: Show issues

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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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Article ; Online: Epidermal growth factor receptor inhibition potentiates chemotherapeutics-mediated sensitization of metastatic breast cancer stem cells.

Kar, Trisha / Dugam, Prachi / Shivhare, Surbhi / Shetty, Swathi R / Choudhury, Subholakshmi / Sen, Debanjan / Deb, Barnali / Majumdar, Swapan / Debnath, Sudhan / Das, Amitava

Cancer reports (Hoboken, N.J.)

2024 Volume 7, Issue 3, Page(s) e2049

Abstract: Background: Metastasis has been a cause of the poor prognosis and cancer relapse of triple-negative breast cancer (TNBC) patients. The metastatic nature of TNBC is contributed by the breast cancer stem cells (CSCs) which have been implicated in ... ...

Abstract	Background: Metastasis has been a cause of the poor prognosis and cancer relapse of triple-negative breast cancer (TNBC) patients. The metastatic nature of TNBC is contributed by the breast cancer stem cells (CSCs) which have been implicated in tumorigenesis. Higher expression of epidermal growth factor receptor (EGFR) in breast CSCs has been used as a molecular target for breast cancer therapeutics. Thus, it necessitates the design and generation of efficacious EGFR inhibitors to target the downstream signaling associated with the cellular proliferation and tumorigenesis of breast cancer. Aim: To generate efficacious EGFR inhibitors that can potentiate the chemotherapeutic-mediated mitigation of breast cancer tumorigenesis. Methods and results: We identified small molecule EGFR inhibitors using molecular docking studies. In-vitro screening of the compounds was undertaken to identify the cytotoxicity profile of the small-molecule EGFR inhibitors followed by evaluation of the non-cytotoxic compounds in modulating the doxorubicin-induced migration, in-vitro tumorigenesis potential, and their effect on the pro-apoptotic genes' and protein markers' expression in TNBC cells. Compound 1e potentiated the doxorubicin-mediated inhibitory effect on proliferation, migration, in-vitro tumorigenesis capacity, and induction of apoptosis in MDA-MB-231 cells, and in the sorted CD24 Conclusion: Thus, the study suggests that EGFR inhibition-mediated sensitization of the aggressive and metastatic breast CSCs in TNBCs toward chemotherapeutics may reduce the relapse of the disease.
MeSH term(s)	Animals ; Humans ; Mice ; Carcinogenesis ; Cell Transformation, Neoplastic ; Doxorubicin/pharmacology ; ErbB Receptors/antagonists & inhibitors ; Mice, Inbred C57BL ; Molecular Docking Simulation ; Neoplasm Recurrence, Local ; Neoplastic Stem Cells ; Recurrence ; Triple Negative Breast Neoplasms/drug therapy
Chemical Substances	Doxorubicin (80168379AG) ; ErbB Receptors (EC 2.7.10.1)
Language	English
Publishing date	2024-03-22
Publishing country	United States
Document type	Journal Article
ISSN	2573-8348
ISSN (online)	2573-8348
DOI	10.1002/cnr2.2049
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Article ; Online: Identification of potential edible mushroom as SARS-CoV-2 main protease inhibitor using rational drug designing approach.

Sen, Debanjan / Debnath, Bimal / Debnath, Pradip / Debnath, Sudhan / Zaki, Magdi E A / Masand, Vijay H

Scientific reports

2022 Volume 12, Issue 1, Page(s) 1503

Abstract: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is highly pathogenic to humans and has created health care threats worldwide. This urgent situation has focused the researchers worldwide towards the development of novel vaccine or small ... ...

Abstract	Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is highly pathogenic to humans and has created health care threats worldwide. This urgent situation has focused the researchers worldwide towards the development of novel vaccine or small molecule therapeutics for SARS-CoV-2. Although several vaccines have already been discovered and are in use for the masses, no therapeutic medication has yet been approved by FDA for the treatment of COVID-19. Keeping this in view, in the present study, we have identified promising hits against the main protease (M
MeSH term(s)	Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Basidiomycota/chemistry ; Benzofurans/pharmacology ; Benzofurans/therapeutic use ; COVID-19/drug therapy ; Coronavirus 3C Proteases/antagonists & inhibitors ; Molecular Dynamics Simulation ; Protease Inhibitors/pharmacology ; Protease Inhibitors/therapeutic use ; SARS-CoV-2/drug effects ; SARS-CoV-2/enzymology ; Terphenyl Compounds/pharmacology ; Terphenyl Compounds/therapeutic use
Chemical Substances	Antiviral Agents ; Benzofurans ; Protease Inhibitors ; Terphenyl Compounds ; kynapcin 12 ; kynapcin-24 ; kynapcin-28 ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2022-01-27
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/s41598-022-05349-x
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Article: Identification of SARS-CoV-2 Main Protease Inhibitors Using Structure Based Virtual Screening and Molecular Dynamics Simulation of DrugBank Database.

Debnath, Pradip / Bhaumik, Samhita / Sen, Debanjan / Muttineni, Ravi K / Debnath, Sudhan

ChemistrySelect

2021 Volume 6, Issue 20, Page(s) 4991–5013

Abstract: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is highly pathogenic to humans and has created an unprecedented global health care threat. Globally, intense efforts are going on to discover a vaccine or new drug molecules to control the ... ...

Abstract	Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is highly pathogenic to humans and has created an unprecedented global health care threat. Globally, intense efforts are going on to discover a vaccine or new drug molecules to control the COVID-19. However, till today, there is no effective therapeutics or treatment available for COVID-19. In this study, we aim to find out potential small molecule inhibitors for SARS-CoV-2 main protease (M
Language	English
Publishing date	2021-06-18
Publishing country	Germany
Document type	Journal Article
ISSN	2365-6549
ISSN	2365-6549
DOI	10.1002/slct.202100854
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