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Article ; Online: Identification of High-Affinity Inhibitors of TANK-Binding Kinase 1 (TBK1): A Promising Frontier for Controlling Inflammatory Signaling in Cancer.

Jairajpuri, Deeba Shamim / Mohammad, Taj / Hussain, Afzal / Alajmi, Mohamed F / Yadav, Dharmendra Kumar / Hassan, Md Imtaiyaz

Discovery medicine

2024 Volume 36, Issue 180, Page(s) 129–139

Abstract: Background: TANK-binding kinase 1 (TBK1) is an important serine/threonine kinase involved in inflammatory signaling pathways, influencing cellular processes such as proliferation, programmed cell death, autophagy, and immune response regulation. ... ...

Abstract	Background: TANK-binding kinase 1 (TBK1) is an important serine/threonine kinase involved in inflammatory signaling pathways, influencing cellular processes such as proliferation, programmed cell death, autophagy, and immune response regulation. Dysregulation of TBK1 has been linked to cancer progression and neurodegenerative disorders, making it an attractive target for therapeutic development. This study aimed to identify potential TBK1 inhibitors using a structure-based virtual screening approach. Methods: We conducted a comprehensive screening of the ZINC database to identify compounds with high binding affinity for TBK1, employing molecular docking as the primary selection criterion. The top candidates were then subjected to extensive 200 ns molecular dynamics (MD) simulations to assess the conformational dynamics of TBK1 and the stability of the protein-ligand complexes, with a focus on ZINC02095133 and ZINC02130647. Results: The findings revealed that TBK1 forms stable complexes with ZINC02095133 and ZINC02130647, demonstrating consistent interactions throughout the MD simulations. This suggests that these compounds hold promise as potential lead molecules for future therapies targeting TBK1. Conclusions: This study identifies ZINC02095133 and ZINC02130647 as promising TBK1 inhibitors with therapeutic potential. However, further experimental validation and optimization are required to develop novel inhibitors for diseased conditions associated with TBK1 signaling. These findings pave the way for future investigations into the clinical utility of these compounds in combating TBK1-related pathologies.
MeSH term(s)	Humans ; Molecular Docking Simulation ; Protein Serine-Threonine Kinases/chemistry ; Protein Serine-Threonine Kinases/metabolism ; Signal Transduction ; Molecular Dynamics Simulation ; Neoplasms/drug therapy
Chemical Substances	Protein Serine-Threonine Kinases (EC 2.7.11.1) ; TBK1 protein, human (EC 2.7.11.1)
Language	English
Publishing date	2024-01-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	2415544-5
ISSN	1944-7930 ; 1944-7930
ISSN (online)	1944-7930
ISSN	1944-7930
DOI	10.24976/Discov.Med.202436180.12
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Iron response elements (IREs)-mRNA of Alzheimer's amyloid precursor protein binding to iron regulatory protein (IRP1): a combined molecular docking and spectroscopic approach.

Khan, Mateen A / Mohammad, Taj / Malik, Ajamaluddin / Hassan, Md Imtaiyaz / Domashevskiy, Artem V

Scientific reports

2023 Volume 13, Issue 1, Page(s) 5073

Abstract: The interaction between the stem-loop structure of the Alzheimer's amyloid precursor protein IRE mRNA and iron regulatory protein was examined by employing molecular docking and multi-spectroscopic techniques. A detailed molecular docking analysis of APP ...

Abstract	The interaction between the stem-loop structure of the Alzheimer's amyloid precursor protein IRE mRNA and iron regulatory protein was examined by employing molecular docking and multi-spectroscopic techniques. A detailed molecular docking analysis of APP IRE mRNA∙IRP1 reveals that 11 residues are involved in hydrogen bonding as the main driving force for the interaction. Fluorescence binding results revealed a strong interaction between APP IRE mRNA and IRP1 with a binding affinity and an average binding sites of 31.3 × 10
MeSH term(s)	Humans ; Alzheimer Disease/metabolism ; Amyloid beta-Protein Precursor/genetics ; Amyloid beta-Protein Precursor/metabolism ; Iron/metabolism ; Iron Regulatory Protein 1/metabolism ; Iron Regulatory Protein 2/genetics ; Iron-Regulatory Proteins/genetics ; Molecular Docking Simulation ; Protein Binding ; Response Elements ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Spectrum Analysis
Chemical Substances	Amyloid beta-Protein Precursor ; Iron (E1UOL152H7) ; Iron Regulatory Protein 1 (EC 4.2.1.3) ; Iron Regulatory Protein 2 (EC 4.2.1.3) ; Iron-Regulatory Proteins ; RNA, Messenger ; ACO1 protein, human (EC 4.2.1.3) ; APP protein, human
Language	English
Publishing date	2023-03-28
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/s41598-023-32073-x
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Article ; Online: Identification of high-affinity pyridoxal kinase inhibitors targeting cancer therapy: an integrated docking and molecular dynamics simulation approach.

Banerjee, Pallabi / Chandra, Anshuman / Mohammad, Taj / Singh, Nagendra / Hassan, Md Imtaiyaz / Qamar, Imteyaz

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–18

Abstract: Pyridoxal kinase (PDXK) is a vitamin B6-dependent transferase enzyme encoded by ... ...

Abstract	Pyridoxal kinase (PDXK) is a vitamin B6-dependent transferase enzyme encoded by the
Language	English
Publishing date	2023-08-14
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2246580
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Article ; Online: Discovering Promising Biomarkers and Therapeutic Targets for Duchenne Muscular Dystrophy: a Multiomics Meta-Analysis Approach.

Elasbali, Abdelbaset Mohamed / Al-Soud, Waleed Abu / Adnan, Mohd / Alhassan, Hassan H / Mohammad, Taj / Hassan, Md Imtaiyaz

Molecular neurobiology

2024

Abstract: Duchenne muscular dystrophy (DMD) is a genetic disorder that causes muscle weakness and degeneration. In this study, we identified potential biomarkers and drug targets for DMD through a comprehensive meta-analysis of mRNA profiles. We conducted an in- ... ...

Abstract	Duchenne muscular dystrophy (DMD) is a genetic disorder that causes muscle weakness and degeneration. In this study, we identified potential biomarkers and drug targets for DMD through a comprehensive meta-analysis of mRNA profiles. We conducted an in-depth analysis of three microarray datasets from the GEO database, utilizing the Affymetrix platform. A rigorous data pre-processing pipeline encompassed background correction, normalization, log2 transformation and probe-to-gene symbol mapping. Robust multi-array average method followed by Limma package in R was employed to ensure differential expression analysis within individual datasets, yielding gene-specific p-values. We identified 63 genes exhibiting statistically significant differential expression across the three datasets (p < 0.05) and an absolute log fold change > 1.5. Functional enrichment analyses of these differentially expressed genes were done, followed by pathway analyses. Our results suggested pertinent biological processes, molecular functions and cellular components associated with DMD. Finally, eight hub genes-COL6A3, COL1A1, COL3A1, COL1A2, POSTN, TIMP1, THBS2 and SPP1-were pinpointed as central players in the network. Two differentially expressed genes with substantial absolute log-fold changes, namely, DMD, downregulated and MYH3, upregulated, were identified as potential therapeutic candidates. In light of these findings, our work contributes not only to understanding DMD at the molecular level but also presents potential targets for therapeutic strategies. Finally, our study facilitates the development of therapeutic interventions that can effectively control and mitigate the impact of DMD.
Language	English
Publishing date	2024-01-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	645020-9
ISSN	1559-1182 ; 0893-7648
ISSN (online)	1559-1182
ISSN	0893-7648
DOI	10.1007/s12035-023-03868-w
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Article ; Online: InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening.

Mohammad, Taj / Mathur, Yash / Hassan, Md Imtaiyaz

Briefings in bioinformatics

2020 Volume 22, Issue 4

Abstract: Exploring protein-ligand interactions is a subject of immense interest, as it provides deeper insights into molecular recognition, mechanism of interaction and subsequent functions. Predicting an accurate model for a protein-ligand interaction is a ... ...

Abstract	Exploring protein-ligand interactions is a subject of immense interest, as it provides deeper insights into molecular recognition, mechanism of interaction and subsequent functions. Predicting an accurate model for a protein-ligand interaction is a challenging task. Molecular docking is a computational method used for predicting the preferred orientation, binding conformations and the binding affinity of a ligand to a macromolecular target, especially protein. It has been applied in 'virtual high-throughput screening' of chemical libraries containing millions of compounds to find potential leads in drug design and discovery. Here, we have developed InstaDock, a free and open access Graphical User Interface (GUI) program that performs molecular docking and high-throughput virtual screening efficiently. InstaDock is a single-click GUI that uses QuickVina-W, a modified version of AutoDock Vina for docking calculations, made especially for the convenience of non-bioinformaticians and for people who are not experts in using computers. InstaDock facilitates onboard analysis of docking and visual results in just a single click. To sum up, InstaDock is the easiest and more interactive interface than ever existing GUIs for molecular docking and high-throughput virtual screening. InstaDock is freely available for academic and industrial research purposes via https://hassanlab.org/instadock.
MeSH term(s)	Algorithms ; Drug Design ; Drug Evaluation, Preclinical ; High-Throughput Screening Assays ; Humans ; Molecular Docking Simulation ; Proteins/chemistry ; Proteins/metabolism ; User-Computer Interface
Chemical Substances	Proteins
Language	English
Publishing date	2020-10-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbaa279
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Article ; Online: Investigating MARK4 inhibitory potential of Bacopaside II: Targeting Alzheimer's disease.

Anwar, Saleha / Mohammad, Taj / Azhar, Md Khabeer / Fatima, Hera / Alam, Afsar / Hasan, Gulam Mustafa / Islam, Asimul / Kaur, Punit / Hassan, Md Imtaiyaz

International journal of biological macromolecules

2023 Volume 245, Page(s) 125364

Abstract: Microtubule affinity regulating kinase 4 (MARK4) is known to hyperphosphorylate tau protein, which subsequently causes Alzheimer's disease (AD). MARK4 is a well-validated drug target for AD; thus, we employed its structural features to discover potential ...

Abstract	Microtubule affinity regulating kinase 4 (MARK4) is known to hyperphosphorylate tau protein, which subsequently causes Alzheimer's disease (AD). MARK4 is a well-validated drug target for AD; thus, we employed its structural features to discover potential inhibitors. On the other hand, complementary and alternative medicines (CAMs) have been used for the treatment of numerous diseases with little side effects. In this regard, Bacopa monnieri extracts have been extensively used to treat neurological disorders because of their neuroprotective roles. The plant extract is used as a memory enhancer and a brain tonic. Bacopaside II is a major component of Bacopa monnieri; thus, we studied its inhibitory effects and binding affinity towards the MARK4. Bacopaside II show a considerable binding affinity for MARK4 (K = 10
MeSH term(s)	Humans ; Alzheimer Disease/drug therapy ; Saponins/pharmacology ; Protein Serine-Threonine Kinases/chemistry ; Microtubules
Chemical Substances	bacopaside II (ZO6L404Y9T) ; Saponins ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; MARK4 protein, human (EC 2.7.1.-)
Language	English
Publishing date	2023-06-13
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.2023.125364
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Article ; Online: Structure-based identification of potential inhibitors of ribosomal protein S6 kinase 1, targeting cancer therapy: a combined docking and molecular dynamics simulations approach.

Alam, Afsar / Khan, Mohammad Shahzeb / Mathur, Yash / Sulaimani, Md Nayab / Farooqui, Naqiya / Ahmad, Sheikh F / Nadeem, Ahmed / Yadav, Dharmendra Kumar / Mohammad, Taj

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–12

Abstract: Ribosomal protein S6 kinase 1 (S6K1), commonly known as P70-S6 kinase 1 (p70S6), is a key protein kinase involved in cellular signaling pathways that regulate cell growth, proliferation, and metabolism. Its significant role is reported in the PIK3/mTOR ... ...

Abstract	Ribosomal protein S6 kinase 1 (S6K1), commonly known as P70-S6 kinase 1 (p70S6), is a key protein kinase involved in cellular signaling pathways that regulate cell growth, proliferation, and metabolism. Its significant role is reported in the PIK3/mTOR signaling pathway and is associated with various complex diseases, including diabetes, obesity, and different types of cancer. Due to its involvement in various physiological and pathological conditions, S6K1 is considered as an attractive target for drug design and discovery. One way to target S6K1 is by developing small molecule inhibitors that specifically bind to its ATP-binding site, preventing its activation and thus inhibiting downstream signaling pathways necessary for cell growth and survival. In this study, we have conducted a multitier virtual screening of a pool of natural compounds to identify potential S6K1 inhibitors. We performed molecular docking on IMPPAT 2.0 library and selected top hits based on their binding affinity, ligand efficiency, and specificity towards S6K1. The selected hits were further assessed based on different filters of drug-likeliness where two compounds (Hecogenin and Glabrene) were identified as potential leads for S6K1 inhibition. Both compounds showed appreciable affinity, ligand efficiency and specificity towards S6K1 binding pocket, drug-like properties, and stable protein-ligand complexes in molecular dynamics (MD) simulations. Finally, our study has suggested that Hecogenin and Glabrene can be potential S6K1 inhibitors which are presumably implicated in the therapeutic management of associated diseases such as diabetes, obesity, and varying types of cancer.Communicated by Ramaswamy H. Sarma.
Language	English
Publishing date	2023-06-26
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2228912
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Article ; Online: An integrated docking and molecular dynamics simulation approach to discover potential inhibitors of activin receptor-like kinase 1.

Jairajpuri, Deeba Shamim / Mohammad, Taj / Hussain, Afzal / Amir, Samira / Fatima, Urooj / AlAjmi, Mohamed F / Yadav, Dharmendra Kumar / Hassan, Md Imtaiyaz

Journal of molecular recognition : JMR

2023 Volume 37, Issue 2, Page(s) e3069

Abstract: Activin receptor-like kinase 1 (ALK1) is a transmembrane receptor involved in crucial signaling pathways associated with angiogenesis and vascular development. Inhibition of ALK1 signaling has emerged as a promising therapeutic strategy for various ... ...

Abstract	Activin receptor-like kinase 1 (ALK1) is a transmembrane receptor involved in crucial signaling pathways associated with angiogenesis and vascular development. Inhibition of ALK1 signaling has emerged as a promising therapeutic strategy for various angiogenesis-related diseases, including cancer and hereditary hemorrhagic telangiectasia. This study aimed to investigate the potential of phytoconstituents as inhibitors of ALK1 using a combined approach of virtual screening and molecular dynamics (MDs) simulations. Phytoconstituents from the IMPPAT 2.0 database underwent virtual screening to identify potential inhibitors of ALK1. The compounds were initially filtered based on physicochemical parameters, following Lipinski's rules and the PAINS filter. Subsequently, compounds demonstrating high binding affinities in docking analysis were further analyzed. Additional assessments, including ADMET, PAINS, and PASS evaluations, were conducted to identify more potent hits. Through interaction analysis, a phytoconstituent, Candidine, exhibited appreciable affinity and specific interactions with the ALK1 active site. To validate the results, MD simulations and principal components analysis were performed. The MD simulations demonstrated that Candidine stabilized the ALK1 structure and reduced conformational fluctuations. In conclusion, Candidine shows promising potential as binding partners of ALK1. These findings provide a foundation for further exploration and development of Candidine as a lead molecule for therapeutic interventions targeting ALK1-associated diseases.
MeSH term(s)	Humans ; Molecular Dynamics Simulation ; Signal Transduction ; Neoplasms ; Molecular Docking Simulation
Language	English
Publishing date	2023-12-06
Publishing country	England
Document type	Journal Article
ZDB-ID	1015084-5
ISSN	1099-1352 ; 0952-3499
ISSN (online)	1099-1352
ISSN	0952-3499
DOI	10.1002/jmr.3069
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Article ; Online: Identification of natural product-based effective inhibitors of spleen tyrosine kinase (SYK) through virtual screening and molecular dynamics simulation approaches.

Ali, Tufail / Anjum, Farah / Choudhury, Arunabh / Shafie, Alaa / Ashour, Amal Adnan / Almalki, Abdulraheem / Mohammad, Taj / Hassan, Md Imtaiyaz

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 7, Page(s) 3459–3471

Abstract: Spleen tyrosine kinase (SYK) is a non-receptor tyrosine kinase that plays an essential role in signal transduction across different cell types. In the context of allergy and autoimmune disorders, it is a crucial regulator of immune receptor signaling in ... ...

Abstract	Spleen tyrosine kinase (SYK) is a non-receptor tyrosine kinase that plays an essential role in signal transduction across different cell types. In the context of allergy and autoimmune disorders, it is a crucial regulator of immune receptor signaling in inflammatory cells such as B cells, mast cells, macrophages, and neutrophils. Developing SYK kinase inhibitors has gained significant interest for potential therapeutic applications in neurological and cancer-related conditions. The clinical use of the most advanced SYK inhibitor, Fostamatinib, has been limited due to its unwanted side effects. Thus, a more targeted approach to SYK inhibition would provide a more comprehensive treatment window. In this study, we used a virtual screening approach to identify potential SYK inhibitors from natural compounds from the IMPPAT database. We identified two compounds, Isolysergic acid and Michelanugine, which showed strong affinity and specificity for the SYK binding pocket. All-atom molecular dynamics (MD) simulations were also performed to explore the stability, conformational changes, and interaction mechanism of SYK in complexes with the identified compounds. The identified compounds might have the potential to be developed into promising SYK inhibitors for the treatment of various diseases, including autoimmune disorders, cancer, and inflammatory diseases. This work aims to identify potential phytochemicals to develop a new protein kinase inhibitor for treating advanced malignancies by providing an updated understanding of the role of SYK.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Syk Kinase ; Protein-Tyrosine Kinases ; Molecular Dynamics Simulation ; Protein Kinase Inhibitors/pharmacology ; Protein Kinase Inhibitors/chemistry ; Autoimmune Diseases ; Neoplasms
Chemical Substances	Syk Kinase (EC 2.7.10.2) ; Protein-Tyrosine Kinases (EC 2.7.10.1) ; Protein Kinase Inhibitors ; SYK protein, human (EC 2.7.10.2)
Language	English
Publishing date	2023-06-01
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2218938
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Article ; Online: Investigating MARK4 inhibitory potential of Bacopaside II: Targeting Alzheimer's disease

Anwar, Saleha / Mohammad, Taj / Azhar, Md. Khabeer / Fatima, Hera / Alam, Afsar / Hasan, Gulam Mustafa / Islam, Asimul / Kaur, Punit / Hassan, Md. Imtaiyaz

International Journal of Biological Macromolecules. 2023 Aug., v. 245 p.125364-

2023

Abstract	Microtubule affinity regulating kinase 4 (MARK4) is known to hyperphosphorylate tau protein, which subsequently causes Alzheimer's disease (AD). MARK4 is a well-validated drug target for AD; thus, we employed its structural features to discover potential inhibitors. On the other hand, complementary and alternative medicines (CAMs) have been used for the treatment of numerous diseases with little side effects. In this regard, Bacopa monnieri extracts have been extensively used to treat neurological disorders because of their neuroprotective roles. The plant extract is used as a memory enhancer and a brain tonic. Bacopaside II is a major component of Bacopa monnieri; thus, we studied its inhibitory effects and binding affinity towards the MARK4. Bacopaside II show a considerable binding affinity for MARK4 (K = 10⁷ M⁻¹) and inhibited kinase activity with an IC₅₀ value of 5.4 μM. To get atomistic insights into the binding mechanism, we performed Molecular dynamics (MD) simulation studies for 100 ns. Bacopaside II binds strongly to the active site pocket residues of MARK4 and a number of hydrogen bonds remain stable throughout the MD trajectory. Our findings provide the basis for the therapeutic implication of Bacopaside and its derivatives in MARK4-related neurodegenerative diseases, especially AD and neuroinflammation.
Keywords	Alzheimer disease ; Bacopa monnieri ; active sites ; brain ; drugs ; hydrogen ; memory ; microtubules ; molecular dynamics ; plant extracts ; therapeutics ; Alzheimer's disease ; Microtubule affinity regulating kinase ; Kinase inhibitors ; Bacopaside ; AD ; MARK4 ; PDB ; MD ; ITC ; RMSD ; RMSF ; Rg ; Bac II ; PCA ; FEL ; SASA
Language	English
Dates of publication	2023-08
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.125364
Database	NAL-Catalogue (AGRICOLA)

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