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Article ; Online: Adsorption behavior of mercaptopurine and 6-thioguanine drugs on the B

Abd El-Mageed, H R / Abbas, Heba S

Journal of biomolecular structure & dynamics

2021 Volume 40, Issue 19, Page(s) 9464–9483

Abstract: Lately, drug delivery systems established on nanostructures have become the most proficient to be studied. There are different studies suggested that the BN nanoclusters can be used as drug carriers and transport drugs in the target cell. Therefore, the ... ...

Abstract	Lately, drug delivery systems established on nanostructures have become the most proficient to be studied. There are different studies suggested that the BN nanoclusters can be used as drug carriers and transport drugs in the target cell. Therefore, the interactions and adsorption behavior of Mercaptopurine (MC) and 6-thioguanine (TG) as anti-cancer drugs on the B
Language	English
Publishing date	2021-08-12
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.1930163
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Article ; Online: Electronic, mechanical, and thermal properties of zirconium dioxide nanotube interacting with poly lactic-co-glycolic acid and chitosan as potential agents in bone tissue engineering: insights from computational approaches.

Almalki, Atiah H / Belal, Amany / Farghali, Ahmed A / Mahmoud, Rehab / Mustafa, F M / Abd El-Mageed, H R

Journal of biomolecular structure & dynamics

2023 Volume 42, Issue 1, Page(s) 231–243

Abstract: For the first time, the interaction of the Poly lactic-co-glycolic acid (PLGA) and Chitosan (CH) with Zirconium dioxide ( ... ...

Abstract	For the first time, the interaction of the Poly lactic-co-glycolic acid (PLGA) and Chitosan (CH) with Zirconium dioxide (ZrO
MeSH term(s)	Tissue Engineering ; Chitosan/chemistry ; Polylactic Acid-Polyglycolic Acid Copolymer ; Tissue Scaffolds/chemistry ; Polyglycolic Acid/chemistry ; Glycols ; Lactic Acid/chemistry ; Nanotubes
Chemical Substances	Chitosan (9012-76-4) ; Polylactic Acid-Polyglycolic Acid Copolymer (1SIA8062RS) ; zirconium oxide (S38N85C5G0) ; Polyglycolic Acid (26009-03-0) ; Glycols ; glycolic acid (0WT12SX38S) ; Lactic Acid (33X04XA5AT)
Language	English
Publishing date	2023-03-30
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2194006
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Article ; Online: Computer-based identification of olive oil components as a potential inhibitor of neirisaral adhesion a regulatory protein.

Al-Shuaeeb, Riyadh Ahmed Atto / Yassin, A A / Ibrahim, Mahmoud A A / Abd El-Mageed, H R / Ghandour, M A / Khalil, M M

Journal of biomolecular structure & dynamics

2022 Volume 41, Issue 5, Page(s) 1553–1560

Abstract: ... In ... ...

Abstract	In silico
MeSH term(s)	Molecular Docking Simulation ; Olive Oil ; Apigenin/pharmacology ; Apigenin/chemistry ; Luteolin/pharmacology ; Luteolin/chemistry ; Ligands ; Molecular Dynamics Simulation
Chemical Substances	Olive Oil ; Apigenin (7V515PI7F6) ; Luteolin (KUX1ZNC9J2) ; Ligands ; erythrodiol (3VWF903FSS)
Language	English
Publishing date	2022-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2021.2022535
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Article ; Online: In silico

Ahmed Atto Al-Shuaeeb, Riyadh / Abd El-Mageed, H R / Ahmed, Shimaa / Mohamed, Hussein S / Hamza, Zeinab S / Rafi, Md Oliullah / Ahmad, Iqrar / Patel, Harun

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 23, Page(s) 14484–14496

Abstract: Microtubule affinity regulating kinase (MARK4) has been proposed as a potential therapeutic target for diabetes, cancer, and neurological diseases. We used a variety of computational studies techniques to examine the binding affinity and MARK4 inhibitory ...

Abstract	Microtubule affinity regulating kinase (MARK4) has been proposed as a potential therapeutic target for diabetes, cancer, and neurological diseases. We used a variety of computational studies techniques to examine the binding affinity and MARK4 inhibitory potential of several isoquinoline alkaloids. MARK4 has been associated with tau protein phosphorylation and, consequently, Alzheimer's disease. The three molecules with the highest binding affinities inside the 5ES1 receptor, according to molecular docking experiments, are isoliensinine, liensinine, and methylcorypalline. Isoliensinine had the highest drug score and drug likeness, coming in at 1.17, while Liensinine and Methylcorypalline came in at 1.15 and 1.07, respectively. The thesis claims that three compounds have a better chance than the others of being identified as therapeutic leads. The bulk of the compounds under investigation didn't break any of Lipinski's five rules, especially methylcorypalline, which did and is probably orally active. The majority of the compounds under investigation, particularly Isoliensinine, Liensinine, and Methylcorypalline, show the potential to exhibit drug-like behaviour, which is strongly confirmed by ADMET characteristics estimates. The chemicals Isoliensinine, Liensinine, and Methylcorypalline, especially Methylcorypalline, form the most stable combination with the 5ES1, according to a 100 ns molecular dynamics simulation of these compounds docked inside 5ES1 complexes. Methylcorypalline has a higher binding affinity inside 5ES1, according to additional MM/GBSA experiments using MD trajectories. Overall, research supports the use of the drug development tool methylcolipalin for its ability to inhibit MARK4, which may have implications for the treatment of neurodegenerative diseases.Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Humans ; Molecular Docking Simulation ; Neurodegenerative Diseases/drug therapy ; Isoquinolines/pharmacology ; Drug Design ; Alkaloids/pharmacology ; Molecular Dynamics Simulation
Chemical Substances	liensinine (2586-96-1) ; Isoquinolines ; Alkaloids
Language	English
Publishing date	2023-05-15
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2212778
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Article ; Online: Identification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg

Al-Shuaeeb, Riyadh Ahmed Atto / Abd El-Mageed, H R / Ahmed, Shimaa A / Mohamed, Hussein S / Hamza, Zeinab S / Rafi, Md Oliullah / Rahman, Md Shahedur

Journal of biomolecular structure & dynamics

2023 Volume 41, Issue 21, Page(s) 11437–11449

Abstract: Pandemic new severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has increased throughout the world. There is no effective treatment against this virus until now. Since its appearance in Wuhan, China in December 2019, SARS-CoV-2 becomes the ... ...

Abstract	Pandemic new severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has increased throughout the world. There is no effective treatment against this virus until now. Since its appearance in Wuhan, China in December 2019, SARS-CoV-2 becomes the largest challenge the world is opposite today, including the discovery of an antiviral drug for this virus. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation and suppression of host innate immune responses. Potential candidates have been identified to show inhibitory effects against Mpro, both in biochemical assays and viral replication in cells. There are different molecules such as lopinavir and favipiravir considerably inhibit the activity of Mpro in vitro. Different studies have shown that structurally improved favipiravir and other similar compounds can inhibit SARS-CoV-2 main protease. In this work, we study the interactions between favipiravir with Mg
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; COVID-19 Drug Treatment ; Molecular Docking Simulation ; Endopeptidases ; Molecular Dynamics Simulation ; Protease Inhibitors/pharmacology ; Antiviral Agents/pharmacology ; Zinc
Chemical Substances	favipiravir (EW5GL2X7E0) ; Endopeptidases (EC 3.4.-) ; Protease Inhibitors ; Antiviral Agents ; Zinc (J41CSQ7QDS)
Language	English
Publishing date	2023-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2022.2162967
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Article ; Online: Cytotoxic activity, molecular docking, pharmacokinetic properties and quantum mechanics calculations of the brown macroalga

Ahmed, Shimaa A / Rahman, Aziz A / Elsayed, Khaled N M / Abd El-Mageed, H R / Mohamed, Hussein S / Ahmed, Sayed A

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 11, Page(s) 3855–3873

Abstract: In this study, nine compounds were isolated, eight of them were isolated for the first time ... ...

Abstract	In this study, nine compounds were isolated, eight of them were isolated for the first time from
MeSH term(s)	Antineoplastic Agents/pharmacology ; Humans ; MCF-7 Cells ; Molecular Docking Simulation ; Plant Extracts/pharmacology ; Seaweed
Chemical Substances	Antineoplastic Agents ; Plant Extracts
Language	English
Publishing date	2020-06-11
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1774418
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Article ; Online: Bis-indole alkaloid caulerpin from a new source

Abdelrheem, Doaa A / Abd El-Mageed, H R / Mohamed, Hussein S / Rahman, Aziz A / Elsayed, Khaled N M / Ahmed, Sayed A

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 14, Page(s) 5137–5147

Abstract: Caulerpin, a bis-indole alkaloid is isolated from a new ... ...

Abstract	Caulerpin, a bis-indole alkaloid is isolated from a new source
MeSH term(s)	Density Functional Theory ; Humans ; Indole Alkaloids ; Indoles ; Molecular Docking Simulation ; Sargassum
Chemical Substances	Indole Alkaloids ; Indoles ; caulerpin (26612-48-6)
Language	English
Publishing date	2020-06-24
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1784285
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Article ; Online: The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease: insights from molecular docking analysis and molecular dynamic simulation.

Abdelrheem, Doaa A / Ahmed, Shimaa A / Abd El-Mageed, H R / Mohamed, Hussein S / Rahman, Aziz A / Elsayed, Khaled N M / Ahmed, Sayed A

Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering

2020 Volume 55, Issue 11, Page(s) 1373–1386

Abstract: This work aimed at evaluating the inhibitory effect of ten natural bioactive compounds (1-10) as potential inhibitors of SARS-CoV-2-3CL main protease (PDB ID: 6LU7) and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT) by molecular docking analysis. The ... ...

Abstract	This work aimed at evaluating the inhibitory effect of ten natural bioactive compounds (1-10) as potential inhibitors of SARS-CoV-2-3CL main protease (PDB ID: 6LU7) and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT) by molecular docking analysis. The inhibitory effect of all studied compounds was studied with compared to some proposed antiviral drugs which currently used in COVID-19 treatment such as chloroquine, hydroxychloroquine, azithromycin, remdesivir, baloxvir, lopinavir, and favipiravir. Homology modeling and sequence alignment was computed to evaluate the similarity between the SARS-CoV-2-3CL main protease and other SARS-CoV receptors. ADMET properties of all studied compounds were computed and reported. Also, molecular dynamic (MD) simulation was performed on the compound which has the highest binding affinity inside 6LU7 obtained from molecular docking analysis to study it is stability inside receptor in explicit water solvent. Based on molecular docking analysis, we found that caulerpin has the highest binding affinity inside all studied receptors compared to other bioactive compounds and studied drugs. Our homology modeling and sequence alignment showed that SARS-CoV main protease (PDB ID: 3TNT) shares high similarity with 3CLpro (96.00%). Also, ADMET properties confirmed that caulerpin obeys Lipinski's rule and passes ADMET property, which make it a promising compound to act as a new safe natural drug against SARS-CoV-2-3CL main protease. Finally, MD simulation confirmed that the complex formed between caulerpin and 3CLpro is stable in water explicit and had no major effect on the flexibility of the protein throughout the simulations and provided a suitable basis for our study. Also, binding free energy between caulerpin and 6LU7 confirmed the efficacy of the caulerpin molecule against SARS-CoV-2 main protease. So, this study suggested that caulerpin could be used as a potential candidate in COVID-19 treatment.
MeSH term(s)	Betacoronavirus/drug effects ; Betacoronavirus/enzymology ; Coronavirus 3C Proteases ; Cysteine Endopeptidases/metabolism ; Indoles/pharmacology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; SARS-CoV-2 ; Viral Nonstructural Proteins/metabolism
Chemical Substances	Indoles ; Viral Nonstructural Proteins ; caulerpin (26612-48-6) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-10-01
Publishing country	England
Document type	Journal Article
ZDB-ID	196584-0
ISSN	1532-4117 ; 0360-1226 ; 1077-1204 ; 1093-4529
ISSN (online)	1532-4117
ISSN	0360-1226 ; 1077-1204 ; 1093-4529
DOI	10.1080/10934529.2020.1826192
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Article: The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease: insights from molecular docking analysis and molecular dynamic simulation

Abdelrheem, Doaa A / Ahmed, Shimaa A / Abd El-Mageed, H. R / Mohamed, Hussein S / Rahman, Aziz A / Elsayed, Khaled N. M / Ahmed, Sayed A

Journal of environmental science and health. 2020 Sept. 30, v. 55, no. 11

2020

Abstract: This work aimed at evaluating the inhibitory effect of ten natural bioactive compounds (1–10) as potential inhibitors of SARS-CoV-2-3CL main protease (PDB ID: 6LU7) and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT) by molecular docking analysis. The ... ...

Abstract	This work aimed at evaluating the inhibitory effect of ten natural bioactive compounds (1–10) as potential inhibitors of SARS-CoV-2-3CL main protease (PDB ID: 6LU7) and SARS-CoV main proteases (PDB IDs: 2GTB and 3TNT) by molecular docking analysis. The inhibitory effect of all studied compounds was studied with compared to some proposed antiviral drugs which currently used in COVID-19 treatment such as chloroquine, hydroxychloroquine, azithromycin, remdesivir, baloxvir, lopinavir, and favipiravir. Homology modeling and sequence alignment was computed to evaluate the similarity between the SARS-CoV-2-3CL main protease and other SARS-CoV receptors. ADMET properties of all studied compounds were computed and reported. Also, molecular dynamic (MD) simulation was performed on the compound which has the highest binding affinity inside 6LU7 obtained from molecular docking analysis to study it is stability inside receptor in explicit water solvent. Based on molecular docking analysis, we found that caulerpin has the highest binding affinity inside all studied receptors compared to other bioactive compounds and studied drugs. Our homology modeling and sequence alignment showed that SARS-CoV main protease (PDB ID: 3TNT) shares high similarity with 3CLpro (96.00%). Also, ADMET properties confirmed that caulerpin obeys Lipinski’s rule and passes ADMET property, which make it a promising compound to act as a new safe natural drug against SARS-CoV-2-3CL main protease. Finally, MD simulation confirmed that the complex formed between caulerpin and 3CLpro is stable in water explicit and had no major effect on the flexibility of the protein throughout the simulations and provided a suitable basis for our study. Also, binding free energy between caulerpin and 6LU7 confirmed the efficacy of the caulerpin molecule against SARS-CoV-2 main protease. So, this study suggested that caulerpin could be used as a potential candidate in COVID-19 treatment.
Keywords	COVID-19 infection ; Gibbs free energy ; Severe acute respiratory syndrome coronavirus 2 ; azithromycin ; chloroquine ; environmental science ; proteinases ; sequence alignment ; solvents
Language	English
Dates of publication	2020-0930
Size	p. 1373-1386.
Publishing place	Taylor & Francis
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	196584-0
ISSN	1532-4117 ; 0360-1226 ; 1077-1204 ; 1093-4529
ISSN (online)	1532-4117
ISSN	0360-1226 ; 1077-1204 ; 1093-4529
DOI	10.1080/10934529.2020.1826192
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: R

Ibrahim, Mahmoud A A / Mohamed, Yasmeen A M / Abd Elhafez, Heba S M / Shehata, Mohammed N I / Soliman, Mahmoud E S / Ahmed, Muhammad Naeem / Abd El-Mageed, H R / Moussa, Nayra A M

Journal of molecular graphics & modelling

2021 Volume 111, Page(s) 108097

Abstract: For the first time, the potentiality of the ... ...

Abstract	For the first time, the potentiality of the sp
MeSH term(s)	Quantum Theory ; Static Electricity ; Thermodynamics
Language	English
Publishing date	2021-11-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2021.108097
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