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Article: Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approaches for a combination therapy.

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

Structural chemistry

2020 Volume 31, Issue 6, Page(s) 2391–2412

Abstract: Presently, the SARS-CoV-2 (COVID-19) pandemic has been spreading throughout the world. Some drugs such as lopinavir, simeprevir, hydroxychloroquine, chloroquine, and amprenavir have been recommended for COVID-19 treatment by some researchers, but these ... ...

Abstract	Presently, the SARS-CoV-2 (COVID-19) pandemic has been spreading throughout the world. Some drugs such as lopinavir, simeprevir, hydroxychloroquine, chloroquine, and amprenavir have been recommended for COVID-19 treatment by some researchers, but these drugs were not effective enough against this virus. This study based on in silico approaches was aimed to increase the anti-COVID-19 activities of these drugs by using caulerpin and its derivatives as an adjunct drug against SARS-CoV-2 receptor proteins: the SARS-CoV-2 main protease and the SARS-CoV-2 spike protein. Caulerpin exhibited antiviral activities against chikungunya virus and herpes simplex virus type 1. Caulerpin and some of its derivatives showed inhibitory activity against Alzheimer's disease. The web server ANCHOR revealed higher protein stability for the two receptors with disordered score (< 0.6). Molecular docking analysis showed that the binding energies of most of the caulerpin derivatives were higher than all the suggested drugs for the two receptors. Also, we deduced that inserting NH
Keywords	covid19
Language	English
Publishing date	2020-07-23
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/s11224-020-01586-w
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Article: Amplexicine, an antioxidant flavan-3-ol from Polygonum amplexicaule.

Tantry, Mudasir A / Rahman, Aziz A

Natural product communications

2011 Volume 6, Issue 11, Page(s) 1597–1598

Abstract: Bioassay guided fractionation of an ethanolic extract of Polygonum amplexicaule D. Don led to the isolation of amplexicine, a new flavan-3-ol (1), along with khellactone (2). The structure of the isolates was established by UV, IR, HRESI/MS and NMR, ... ...

Abstract	Bioassay guided fractionation of an ethanolic extract of Polygonum amplexicaule D. Don led to the isolation of amplexicine, a new flavan-3-ol (1), along with khellactone (2). The structure of the isolates was established by UV, IR, HRESI/MS and NMR, including 1D and 2D experiments. Compound 1 exhibited considerable antioxidant activity in a 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging assay.
MeSH term(s)	Antioxidants/analysis ; Flavonoids/chemistry ; Flavonoids/isolation & purification ; Molecular Structure ; Polygonum/chemistry
Chemical Substances	Antioxidants ; Flavonoids ; amplexicine ; flavan-3-ol (35HDD3NRIE)
Language	English
Publishing date	2011-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1934-578X
ISSN	1934-578X
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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: Combination and tricombination therapy to destabilize the structural integrity of COVID-19 by some bioactive compounds with antiviral drugs: insights from molecular docking study.

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

Structural chemistry

2021 Volume 32, Issue 4, Page(s) 1415–1430

Abstract: Recently, the SARS-CoV-2 (COVID-19) pandemic virus has been spreading throughout the world. Until now, no certified drugs have been discovered to efficiently inhibit the virus. The scientists are struggling to find new safe bioactive inhibitors of this ... ...

Abstract	Recently, the SARS-CoV-2 (COVID-19) pandemic virus has been spreading throughout the world. Until now, no certified drugs have been discovered to efficiently inhibit the virus. The scientists are struggling to find new safe bioactive inhibitors of this deadly virus. In this study, we aim to find antagonists that may inhibit the activity of the three major viral targets: SARS-CoV-2 3-chymotrypsin-like protease (6LU7), SARS-CoV-2 spike protein (6VYB), and a host target human angiotensin-converting enzyme 2 (ACE2) receptor (1R42), which is the entry point for the viral encounter, were studied with the prospects of identifying significant drug candidate(s) against COVID-19 infection. Then, the protein stability produced score of less than 0.6 for all residues of all studied receptors. This confirmed that these receptors are extremely stable proteins, so it is very difficult to unstable the stability of these proteins through utilizing individual drugs. Hence, we studied the combination and tricombination therapy between bioactive compounds which have the best binding affinity and some antiviral drugs like chloroquine, hydroxychloroquine, azithromycin, simeprevir, baloxavir, lopinavir, and favipiravir to show the effect of combination and tricombination therapy to disrupt the stability of the three major viral targets that are mentioned previously. Also, ADMET study suggested that most of all studied bioactive compounds are safe and nontoxic compounds. All results confirmed that caulerpin can be utilized as a combination and tricombination therapy along with the studied antiviral drugs for disrupting the stability of the three major viral receptors (6LU7, 6VYB, and 1R42). Supplementary information: The online version contains supplementary material available at 10.1007/s11224-020-01723-5.
Language	English
Publishing date	2021-01-08
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/s11224-020-01723-5
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Article: Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approaches for a combination therapy

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

Struct Chem

Abstract	Presently, the SARS-CoV-2 (COVID-19) pandemic has been spreading throughout the world. Some drugs such as lopinavir, simeprevir, hydroxychloroquine, chloroquine, and amprenavir have been recommended for COVID-19 treatment by some researchers, but these drugs were not effective enough against this virus. This study based on in silico approaches was aimed to increase the anti-COVID-19 activities of these drugs by using caulerpin and its derivatives as an adjunct drug against SARS-CoV-2 receptor proteins: the SARS-CoV-2 main protease and the SARS-CoV-2 spike protein. Caulerpin exhibited antiviral activities against chikungunya virus and herpes simplex virus type 1. Caulerpin and some of its derivatives showed inhibitory activity against Alzheimer's disease. The web server ANCHOR revealed higher protein stability for the two receptors with disordered score (< 0.6). Molecular docking analysis showed that the binding energies of most of the caulerpin derivatives were higher than all the suggested drugs for the two receptors. Also, we deduced that inserting NH2, halogen, and vinyl groups can increase the binding affinity of caulerpin toward 6VYB and 6LU7, while inserting an alkyl group decreases the binding affinity of caulerpin toward 6VYB and 6LU7. So, we can modify the inhibitory effect of caulerpin against 6VYB and 6LU7 by inserting NH2, halogen, and vinyl groups. Based on the protein disordered results, the SARS-CoV-2 main protease and SARS-CoV-2 spike protein domain are highly stable proteins, so it is quite difficult to unstabilize their integrity by using individual drugs. Also, molecular dynamics (MD) simulation indicates that binding of the combination therapy of simeprevir and the candidate studied compounds to the receptors was stable and had no major effect on the flexibility of the protein throughout the simulations and provided a suitable basis for our study. So, this study suggested that caulerpin and its derivatives could be used as a combination therapy along with lopinavir, simeprevir, hydroxychloroquine, chloroquine, and amprenavir for disrupting the stability of SARS-CoV2 receptor proteins to increase the antiviral activity of these drugs.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #669618
Database	COVID19

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Article ; Online: Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs

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

Structural Chemistry ; ISSN 1040-0400 1572-9001

An in silico approaches for a combination therapy

2020

Keywords	Physical and Theoretical Chemistry ; Condensed Matter Physics ; covid19
Language	English
Publisher	Springer Science and Business Media LLC
Publishing country	us
Document type	Article ; Online
DOI	10.1007/s11224-020-01586-w
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The inhibitory effect of some natural bioactive compounds against SARS-CoV-2 main protease

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

insights from molecular docking analysis and molecular dynamic simulation

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

Keywords	Environmental Engineering ; General Medicine ; covid19
Language	English
Publisher	Informa UK Limited
Publishing country	uk
Document type	Article ; Online
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	BASE - Bielefeld Academic Search Engine (life sciences selection)

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